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PDBsum entry 3kcl

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Isomerase PDB id
3kcl
Jmol
Contents
Protein chain
388 a.a.
Ligands
GLC
DOD ×199
Metals
_CD ×2
HEADER    ISOMERASE                               21-OCT-09   3KCL
TITLE     ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX
TITLE    2 WITH TWO CD2+ CATIONS AND D12-D-ALPHA-GLUCOSE IN THE RING FORM
TITLE    3 (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBM)
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: XYLOSE ISOMERASE;
COMPND   3 CHAIN: A;
COMPND   4 EC: 5.3.1.5;
COMPND   5 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS;
SOURCE   3 ORGANISM_TAXID: 1929;
SOURCE   4 GENE: XYLA
KEYWDS    XYLOSE ISOMERASE, DEUTERATED GLUCOSE, CARBOHYDRATE METABOLISM, METAL-
KEYWDS   2 BINDING, PENTOSE SHUNT, XYLOSE METABOLISM, ISOMERASE
EXPDTA    NEUTRON DIFFRACTION; X-RAY DIFFRACTION
AUTHOR    A.Y.KOVALEVSKY,P.LANGAN
REVDAT   4   07-MAR-12 3KCL    1       JRNL
REVDAT   3   27-JUL-11 3KCL    1       REMARK REVDAT
REVDAT   2   13-JUL-11 3KCL    1       VERSN
REVDAT   1   16-JUN-10 3KCL    0
JRNL        AUTH   A.Y.KOVALEVSKY,L.HANSON,S.Z.FISHER,M.MUSTYAKIMOV,S.A.MASON,
JRNL        AUTH 2 V.T.FORSYTH,M.P.BLAKELEY,D.A.KEEN,T.WAGNER,H.L.CARRELL,
JRNL        AUTH 3 A.K.KATZ,J.P.GLUSKER,P.LANGAN
JRNL        TITL   METAL ION ROLES AND THE MOVEMENT OF HYDROGEN DURING REACTION
JRNL        TITL 2 CATALYZED BY D-XYLOSE ISOMERASE: A JOINT X-RAY AND NEUTRON
JRNL        TITL 3 DIFFRACTION STUDY.
JRNL        REF    STRUCTURE                     V.  18   688 2010
JRNL        REFN                   ISSN 0969-2126
JRNL        PMID   20541506
JRNL        DOI    10.1016/J.STR.2010.03.011
REMARK   2
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : NCNS
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK   3               : READ,RICE,SIMONSON,WARREN,MUSTYAKIMOV,
REMARK   3               : AFONINE,LANGAN
REMARK   3
REMARK   3  NEUTRON DATA.
REMARK   3
REMARK   3  REFINEMENT TARGET : NULL
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.500
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : 20875
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL
REMARK   3   R VALUE            (WORKING SET) : 0.188
REMARK   3   FREE R VALUE                     : 0.211
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.400
REMARK   3   FREE R VALUE TEST SET COUNT      : 926
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3054
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 14
REMARK   3   SOLVENT ATOMS            : 199
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : 0.012
REMARK   3   BOND ANGLES            (DEGREES) : 1.45
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   3
REMARK   3  X-RAY DATA.
REMARK   3
REMARK   3  REFINEMENT TARGET : NULL
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.500
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : NULL
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.173
REMARK   3   FREE R VALUE                     : 0.194
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.900
REMARK   3   FREE R VALUE TEST SET COUNT      : 1430
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3054
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 14
REMARK   3   SOLVENT ATOMS            : 199
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : NULL
REMARK   3   BOND ANGLES            (DEGREES) : NULL
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED : NULL
REMARK   3   KSOL        : NULL
REMARK   3   BSOL        : NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3KCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-09.
REMARK 100 THE RCSB ID CODE IS RCSB055822.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 15-JAN-09
REMARK 200  TEMPERATURE           (KELVIN) : 293
REMARK 200  PH                             : 7.7
REMARK 200  NUMBER OF CRYSTALS USED        : NULL
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU FR-E DW
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.54
REMARK 200  MONOCHROMATOR                  : MIRRORS
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IV++
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : RETREAT
REMARK 200  DATA SCALING SOFTWARE          : RETREAT
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : NULL
REMARK 200  RESOLUTION RANGE HIGH      (A) : NULL
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : NULL
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : NULL
REMARK 200  COMPLETENESS FOR SHELL     (%) : NULL
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NCNS
REMARK 200 STARTING MODEL: 3CWH
REMARK 200
REMARK 200 REMARK: NULL
REMARK 230
REMARK 230 EXPERIMENTAL DETAILS
REMARK 230  EXPERIMENT TYPE                : NEUTRON DIFFRACTION
REMARK 230  DATE OF DATA COLLECTION        : 05-APR-09
REMARK 230  TEMPERATURE           (KELVIN) : 293.0
REMARK 230  PH                             : 7.70
REMARK 230  NUMBER OF CRYSTALS USED        : 1
REMARK 230
REMARK 230  NEUTRON SOURCE                 : NUCLEAR REACTOR
REMARK 230  BEAMLINE                       : D19
REMARK 230  WAVELENGTH OR RANGE        (A) : 2.422
REMARK 230  MONOCHROMATOR                  : GRAPHITE
REMARK 230  OPTICS                         : NULL
REMARK 230
REMARK 230  DETECTOR TYPE                  : AREA DETECTOR
REMARK 230  DETECTOR MANUFACTURER          : POSITION-SENSITIVE HE3 NEUTRON
REMARK 230                                   DETECTOR
REMARK 230  INTENSITY-INTEGRATION SOFTWARE : RETREAT
REMARK 230  DATA SCALING SOFTWARE          : RETREAT
REMARK 230
REMARK 230  NUMBER OF UNIQUE REFLECTIONS   : 20875
REMARK 230  RESOLUTION RANGE HIGH      (A) : 2.000
REMARK 230  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 230  REJECTION CRITERIA  (SIGMA(I)) : 1.400
REMARK 230
REMARK 230 OVERALL.
REMARK 230  COMPLETENESS FOR RANGE     (%) : 72.0
REMARK 230  DATA REDUNDANCY                : NULL
REMARK 230  R MERGE                    (I) : NULL
REMARK 230  R SYM                      (I) : NULL
REMARK 230   FOR THE DATA SET  : NULL
REMARK 230
REMARK 230 IN THE HIGHEST RESOLUTION SHELL.
REMARK 230  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 230  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.10
REMARK 230  COMPLETENESS FOR SHELL     (%) : 76.3
REMARK 230  DATA REDUNDANCY IN SHELL       : 1.90
REMARK 230  R MERGE FOR SHELL          (I) : NULL
REMARK 230  R SYM FOR SHELL            (I) : NULL
REMARK 230   FOR SHELL         : 1.300
REMARK 230
REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 230 SOFTWARE USED : NCNS
REMARK 230 STARTING MODEL: 3CWH
REMARK 230
REMARK 230 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 55.84
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES, 40% V/V (NH4)2SO4 (SAT.),
REMARK 280  PROTEIN 40 MG/ML, PH=7.7, BATCH METHOD, APO-XI CRYSTALS WERE WITH
REMARK 280  5MM CDCL2 SALT, 0.5M PER-DEUTERATED D-GLUCOSE IN D2O, TEMPERATURE
REMARK 280  293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z
REMARK 290       3555   -X,Y,-Z
REMARK 290       4555   X,-Y,-Z
REMARK 290       5555   X+1/2,Y+1/2,Z+1/2
REMARK 290       6555   -X+1/2,-Y+1/2,Z+1/2
REMARK 290       7555   -X+1/2,Y+1/2,-Z+1/2
REMARK 290       8555   X+1/2,-Y+1/2,-Z+1/2
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   5  1.000000  0.000000  0.000000       47.09800
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       49.71500
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       51.49300
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       47.09800
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       49.71500
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       51.49300
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       47.09800
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       49.71500
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       51.49300
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       47.09800
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       49.71500
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       51.49300
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 31380 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 47220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -197.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000
REMARK 350   BIOMT1   3 -1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   3  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   3  0.000000  0.000000 -1.000000     -102.98600
REMARK 350   BIOMT1   4  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   4  0.000000 -1.000000  0.000000        0.00000
REMARK 350   BIOMT3   4  0.000000  0.000000 -1.000000     -102.98600
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 O    DOD A1198  LIES ON A SPECIAL POSITION.
REMARK 450
REMARK 450 SOURCE
REMARK 450 THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE
REMARK 500   DD1  HIS A   382     O    DOD A  1061              1.58
REMARK 500   OG1  THR A    91     DH   TYR A   134              1.59
REMARK 500   OD1  ASP A   190     D1   DOD A  1064              1.59
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    VAL A  98   CB  -  CA  -  C   ANGL. DEV. = -17.5 DEGREES
REMARK 500    ARG A 266   NE  -  CZ  -  NH1 ANGL. DEV. =   4.7 DEGREES
REMARK 500    ARG A 266   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.8 DEGREES
REMARK 500    ARG A 340   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.9 DEGREES
REMARK 500    ARG A 387   NE  -  CZ  -  NH2 ANGL. DEV. =  -8.3 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    THR A  17      -74.03    -84.42
REMARK 500    PHE A  94      -27.08   -141.13
REMARK 500    GLU A 186      106.63     73.69
REMARK 500    ASN A 247     -168.86   -171.82
REMARK 500    LYS A 253     -172.33   -175.72
REMARK 500    ALA A 343       66.08   -151.28
REMARK 500    PHE A 357      -70.41   -155.48
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        RMS     TYPE
REMARK 500    ARG A 387         0.11    SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    VAL A 111        17.0      L          L   OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CD A 392  CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 181   OE2
REMARK 620 2 GLU A 217   OE1  93.7
REMARK 620 3 ASP A 245   OD2 103.2 120.0
REMARK 620 4 ASP A 287   OD2 158.6  84.3  96.1
REMARK 620 5 GLC A 401   O4   85.7 155.2  84.1  87.3
REMARK 620 6 GLC A 401   O3   81.9  86.9 151.7  76.7  68.4
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CD A 391  CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 217   OE2
REMARK 620 2 HIS A 220   NE2  82.1
REMARK 620 3 ASP A 255   OD1  92.4  91.8
REMARK 620 4 ASP A 255   OD2 144.7  93.2  52.7
REMARK 620 5 ASP A 257   OD1  87.7 166.0  79.0  89.5
REMARK 620 6 DOD A1001   O   125.6 102.7 140.6  89.6  91.1
REMARK 620 7 GLU A 217   OE1  51.5  74.1 142.1 159.0 106.8  77.3
REMARK 620 N                    1     2     3     4     5     6
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 391
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 392
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLC A 401
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3KBJ   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE X-RAY STRUCTURE OF APO-D-XYLOSE ISOMERASE
REMARK 900 RELATED ID: 3KBM   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE X-RAY STRUCTURE OF D-XYLOSE ISOMERASE
REMARK 900 COMPLEXED WITH 2CD(2+) CO-FACTORS AND D12-D-ALPHA-GLUCOSE
REMARK 900 IN THE CYCLIC FORM
REMARK 900 RELATED ID: 3KBN   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX
REMARK 900 WITH 2NI(2+) CO-FACTORS AND D12-D-GLUCOSE IN THE LINEAR FORM
REMARK 900 RELATED ID: 3KBS   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE X-RAY STRUCTURE OF D-XYLOSE ISOMERASE IN
REMARK 900 COMPLEX WITH 2CD(2+) CO-FACTORS
REMARK 900 RELATED ID: 3KBV   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX
REMARK 900 WITH 2NI(2+) CO-FACTORS
REMARK 900 RELATED ID: 3KBW   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE X-RAY MIXED-METAL STRUCTURE OF D-XYLOSE
REMARK 900 ISOMERASE IN COMPLEX WITH NI(2+) AND MG(2+) CO-FACTORS
REMARK 900 RELATED ID: 3KCJ   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE NEUTRON STRUCTURE OF APO-D-XYLOSE
REMARK 900 ISOMERASE (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBJ)
REMARK 900 RELATED ID: 3KCO   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN
REMARK 900 COMPLEX WITH TWO NI2+ CATIONS AND D12-D-GLUCOSE IN THE
REMARK 900 LINEAR FORM (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBN)
DBREF  3KCL A    1   388  UNP    P24300   XYLA_STRRU       1    388
SEQRES   1 A  388  MET ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE
SEQRES   2 A  388  GLY LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE
SEQRES   3 A  388  GLY ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER
SEQRES   4 A  388  VAL ARG ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR
SEQRES   5 A  388  PHE HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP
SEQRES   6 A  388  SER GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA
SEQRES   7 A  388  LEU ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR
SEQRES   8 A  388  ASN LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE
SEQRES   9 A  388  THR ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG
SEQRES  10 A  388  LYS THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY
SEQRES  11 A  388  ALA GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA
SEQRES  12 A  388  GLU SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP
SEQRES  13 A  388  ARG MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL
SEQRES  14 A  388  THR SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO
SEQRES  15 A  388  LYS PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR
SEQRES  16 A  388  VAL GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG
SEQRES  17 A  388  PRO GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU
SEQRES  18 A  388  GLN MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN
SEQRES  19 A  388  ALA LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN
SEQRES  20 A  388  GLY GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE
SEQRES  21 A  388  GLY ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP
SEQRES  22 A  388  LEU LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE
SEQRES  23 A  388  ASP PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL
SEQRES  24 A  388  TRP ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE
SEQRES  25 A  388  LEU LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU
SEQRES  26 A  388  VAL GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU
SEQRES  27 A  388  ALA ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU
SEQRES  28 A  388  ASP ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA
SEQRES  29 A  388  ALA ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN
SEQRES  30 A  388  LEU ALA MET ASP HIS LEU LEU GLY ALA ARG GLY
HET     CD  A 391       1
HET     CD  A 392       1
HET    GLC  A 401      24
HETNAM      CD CADMIUM ION
HETNAM     GLC ALPHA-D-GLUCOSE
FORMUL   2   CD    2(CD 2+)
FORMUL   4  GLC    C6 H12 O6
FORMUL   5  DOD   *199(D2 O)
HELIX    1   1 THR A    6  ASP A    9  5                                   4
HELIX    2   2 LEU A   15  GLY A   19  1                                   5
HELIX    3   3 ASP A   35  GLY A   47  1                                  13
HELIX    4   4 ASP A   55  ILE A   59  1                                   5
HELIX    5   5 SER A   64  GLY A   83  1                                  20
HELIX    6   6 HIS A   96  LYS A  100  5                                   5
HELIX    7   7 ASP A  108  GLY A  130  1                                  23
HELIX    8   8 SER A  145  LYS A  149  5                                   5
HELIX    9   9 ASP A  150  GLY A  173  1                                  24
HELIX   10  10 THR A  195  GLU A  204  1                                  10
HELIX   11  11 ARG A  208  GLU A  210  5                                   3
HELIX   12  12 GLU A  217  MET A  223  1                                   7
HELIX   13  13 ASN A  227  ALA A  238  1                                  12
HELIX   14  14 ASP A  264  ALA A  278  1                                  15
HELIX   15  15 ASP A  295  ASP A  323  1                                  29
HELIX   16  16 ASP A  323  SER A  333  1                                  11
HELIX   17  17 ARG A  334  ALA A  339  1                                   6
HELIX   18  18 GLY A  346  ASP A  353  1                                   8
HELIX   19  19 ARG A  354  PHE A  357  5                                   4
HELIX   20  20 ASP A  361  ARG A  368  1                                   8
HELIX   21  21 ALA A  371  LEU A  384  1                                  14
SHEET    1   A 8 TYR A 212  VAL A 214  0
SHEET    2   A 8 ARG A 177  ILE A 180  1  N  ILE A 180   O  GLY A 213
SHEET    3   A 8 THR A 133  ALA A 136  1  N  TYR A 134   O  ARG A 177
SHEET    4   A 8 MET A  88  THR A  90  1  N  ALA A  89   O  VAL A 135
SHEET    5   A 8 GLY A  50  HIS A  54  1  N  PHE A  53   O  THR A  90
SHEET    6   A 8 PHE A  11  GLY A  14  1  N  PHE A  13   O  THR A  52
SHEET    7   A 8 ARG A 284  PHE A 286  1  O  PHE A 286   N  THR A  12
SHEET    8   A 8 ASP A 245  LEU A 246  1  N  LEU A 246   O  HIS A 285
SHEET    1   B 2 GLY A 142  ALA A 143  0
SHEET    2   B 2 ASP A 190  ILE A 191 -1  O  ASP A 190   N  ALA A 143
LINK         OE2 GLU A 181                CD    CD A 392     1555   1555  2.18
LINK         OE1 GLU A 217                CD    CD A 392     1555   1555  2.42
LINK         OE2 GLU A 217                CD    CD A 391     1555   1555  2.35
LINK         NE2 HIS A 220                CD    CD A 391     1555   1555  2.37
LINK         OD2 ASP A 245                CD    CD A 392     1555   1555  2.23
LINK         OD1 ASP A 255                CD    CD A 391     1555   1555  2.57
LINK         OD2 ASP A 255                CD    CD A 391     1555   1555  2.38
LINK         OD1 ASP A 257                CD    CD A 391     1555   1555  2.43
LINK         OD2 ASP A 287                CD    CD A 392     1555   1555  2.24
LINK        CD    CD A 391                 O   DOD A1001     1555   1555  2.31
LINK        CD    CD A 392                 O4  GLC A 401     1555   1555  2.47
LINK        CD    CD A 392                 O3  GLC A 401     1555   1555  2.43
LINK         OE1 GLU A 217                CD    CD A 391     1555   1555  2.62
CISPEP   1 GLU A  186    PRO A  187          0        23.42
SITE     1 AC1  5 GLU A 217  HIS A 220  ASP A 255  ASP A 257
SITE     2 AC1  5 DOD A1001
SITE     1 AC2  5 GLU A 181  GLU A 217  ASP A 245  ASP A 287
SITE     2 AC2  5 GLC A 401
SITE     1 AC3 18 TRP A  16  PHE A  26  HIS A  54  THR A  90
SITE     2 AC3 18 PHE A  94  VAL A 135  TRP A 137  GLU A 181
SITE     3 AC3 18 GLU A 217  HIS A 220  ASP A 245  ASP A 287
SITE     4 AC3 18  CD A 392  DOD A1001  DOD A1095  DOD A1105
SITE     5 AC3 18 DOD A1106  DOD A1159
CRYST1   94.196   99.430  102.986  90.00  90.00  90.00 I 2 2 2       8
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.010616  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010057  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009710        0.00000
      
PROCHECK
Go to PROCHECK summary
 References