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PDBsum entry 3kbn

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Isomerase PDB id
3kbn
Jmol
Contents
Protein chain
388 a.a.
Ligands
GLO
Metals
_NI ×3
Waters ×341
HEADER    ISOMERASE                               20-OCT-09   3KBN
TITLE     ROOM TEMPERATURE STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH
TITLE    2 2NI(2+) CO-FACTORS AND D12-D-GLUCOSE IN THE LINEAR FORM
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: XYLOSE ISOMERASE;
COMPND   3 CHAIN: A;
COMPND   4 EC: 5.3.1.5;
COMPND   5 ENGINEERED: YES;
COMPND   6 OTHER_DETAILS: THE PROTEIN WAS PURCHASED FROM HAMPTON RESEARCH
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS;
SOURCE   3 ORGANISM_TAXID: 1929;
SOURCE   4 GENE: XYLA
KEYWDS    XYLOSE ISOMERASE, LINEAR D-GLUCOSE, CARBOHYDRATE METABOLISM, METAL-
KEYWDS   2 BINDING, PENTOSE SHUNT, XYLOSE METABOLISM, ISOMERASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    A.Y.KOVALEVSKY,L.HANSON,P.LANGAN
REVDAT   2   07-MAR-12 3KBN    1       JRNL   VERSN
REVDAT   1   16-JUN-10 3KBN    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.    1.53 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : SHELXL-97
REMARK   3   AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.2
REMARK   3   CROSS-VALIDATION METHOD           : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.141
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.138
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.181
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 3619
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 72268
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 0.130
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : 0.127
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : 0.167
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : 3101
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 61655
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS      : 3053
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 15
REMARK   3   SOLVENT ATOMS      : 341
REMARK   3
REMARK   3  MODEL REFINEMENT.
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 3360.50
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 0.00
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 5
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 30754
REMARK   3   NUMBER OF RESTRAINTS                     : 37993
REMARK   3
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3   BOND LENGTHS                         (A) : 0.012
REMARK   3   ANGLE DISTANCES                      (A) : 0.028
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : 0.023
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.055
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.068
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.018
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : 0.004
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : 0.061
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : 0.090
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED: NULL
REMARK   3
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER
REMARK   3   SPECIAL CASE: NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3KBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-09.
REMARK 100 THE RCSB ID CODE IS RCSB055789.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 10-MAR-09
REMARK 200  TEMPERATURE           (KELVIN) : 293
REMARK 200  PH                             : 7.7
REMARK 200  NUMBER OF CRYSTALS USED        : 1
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                  : VARIMAX 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 : CRYSTALCLEAR
REMARK 200  DATA SCALING SOFTWARE          : CRYSTALCLEAR
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 61655
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.530
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 85.0
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) : 1.53
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.58
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.5
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: SHELX
REMARK 200 STARTING MODEL: 1XIB
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 55.81
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 40MG/ML PROTEIN, 5MM NICL2, 500MM D12-
REMARK 280  D-GLUCOSE 30% (V/V) AMMONIUM SULFATE (SAT.), PH 7.7, TEMPERATURE
REMARK 280  290K
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       47.00350
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       49.83450
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       51.43100
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       47.00350
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       49.83450
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       51.43100
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       47.00350
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       49.83450
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       51.43100
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       47.00350
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       49.83450
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       51.43100
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: 30480 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 47550 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 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     -102.86200
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     -102.86200
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      HOH A1192  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: 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    TYR A   3   C   -  N   -  CA  ANGL. DEV. =  34.3 DEGREES
REMARK 500    ARG A  42   CD  -  NE  -  CZ  ANGL. DEV. =  15.5 DEGREES
REMARK 500    ARG A  42   NE  -  CZ  -  NH1 ANGL. DEV. =   4.0 DEGREES
REMARK 500    ARG A  42   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.3 DEGREES
REMARK 500    ARG A  68   NE  -  CZ  -  NH2 ANGL. DEV. =   4.8 DEGREES
REMARK 500    ARG A  76   CD  -  NE  -  CZ  ANGL. DEV. =  -9.6 DEGREES
REMARK 500    ARG A 112   NE  -  CZ  -  NH1 ANGL. DEV. =  -4.1 DEGREES
REMARK 500    ARG A 152   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.8 DEGREES
REMARK 500    ARG A 208   NE  -  CZ  -  NH1 ANGL. DEV. =  -4.7 DEGREES
REMARK 500    ARG A 266   CD  -  NE  -  CZ  ANGL. DEV. =  12.5 DEGREES
REMARK 500    ARG A 266   NE  -  CZ  -  NH1 ANGL. DEV. =   4.1 DEGREES
REMARK 500    ARG A 266   NE  -  CZ  -  NH2 ANGL. DEV. =  -5.4 DEGREES
REMARK 500    TYR A 310   CB  -  CG  -  CD1 ANGL. DEV. =   3.8 DEGREES
REMARK 500    ARG A 331   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.6 DEGREES
REMARK 500    ARG A 340   CD  -  NE  -  CZ  ANGL. DEV. =  20.6 DEGREES
REMARK 500    ARG A 340   NE  -  CZ  -  NH1 ANGL. DEV. =   6.0 DEGREES
REMARK 500    ARG A 340   NE  -  CZ  -  NH2 ANGL. DEV. =  -5.9 DEGREES
REMARK 500    ARG A 387   CD  -  NE  -  CZ  ANGL. DEV. =   8.5 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      -72.56    -82.63
REMARK 500    PHE A  94      -23.42   -142.18
REMARK 500    GLU A 186      107.65     81.36
REMARK 500    ASN A 247     -166.13   -167.28
REMARK 500    ALA A 343       59.80   -149.31
REMARK 500    PHE A 357      -69.63   -159.37
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500                                 MODEL     OMEGA
REMARK 500 ASN A    2     TYR A    3                 -147.15
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                              NI A 393  NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 181   OE2
REMARK 620 2 GLU A 217   OE1  96.6
REMARK 620 3 ASP A 245   OD2  95.5 104.2
REMARK 620 4 ASP A 287   OD2 160.7  94.6  97.0
REMARK 620 5 GLO A 401   O4   85.0 167.0  88.5  80.6
REMARK 620 6 GLO A 401   O2   82.7  80.9 174.8  83.6  86.5
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              NI A 391  NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 217   OE2
REMARK 620 2 HIS A 220   NE2  80.0
REMARK 620 3 GLO A 401   O1  166.8  94.3
REMARK 620 4 GLO A 401   O2  111.9 109.4  81.1
REMARK 620 5 HOH A1001   O    95.5 166.2  87.3  84.4
REMARK 620 N                    1     2     3     4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              NI A 392  NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 217   OE2
REMARK 620 2 HIS A 220   NE2  72.3
REMARK 620 3 ASP A 255   OD1 117.3 100.3
REMARK 620 4 ASP A 255   OD2 176.2 105.9  66.1
REMARK 620 5 ASP A 257   OD1  94.3 165.5  80.8  87.8
REMARK 620 6 HOH A1001   O    83.2  96.6 156.6  93.7  87.0
REMARK 620 N                    1     2     3     4     5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 391
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 392
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 393
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLO 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: 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: 3KCL   RELATED DB: PDB
REMARK 900 ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN
REMARK 900 COMPLEX WITH TWO CD2+ CATIONS AND D12-D-ALPHA-GLUCOSE IN
REMARK 900 THE RING FORM (REFINED JOINTLY WITH X-RAY STRUCTURE 3KBM)
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  3KBN 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     NI  A 391       1
HET     NI  A 392       1
HET     NI  A 393       1
HET    GLO  A 401      12
HETNAM      NI NICKEL (II) ION
HETNAM     GLO D-GLUCOSE IN LINEAR FORM
FORMUL   2   NI    3(NI 2+)
FORMUL   5  GLO    C6 H12 O6
FORMUL   6  HOH   *341(H2 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  LEU A  129  1                                  22
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  GLY A  239  1                                  13
HELIX   14  14 ASP A  264  GLY A  279  1                                  16
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  GLY A  385  1                                  15
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  ALA A 136   O  ALA A 179
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                NI    NI A 393     1555   1555  2.02
LINK         OE1 GLU A 217                NI    NI A 393     1555   1555  2.08
LINK         OE2 GLU A 217                NI    NI A 391     1555   1555  2.34
LINK         OE2 GLU A 217                NI    NI A 392     1555   1555  2.16
LINK         NE2 HIS A 220                NI    NI A 391     1555   1555  1.98
LINK         NE2 HIS A 220                NI    NI A 392     1555   1555  2.54
LINK         OD2 ASP A 245                NI    NI A 393     1555   1555  2.19
LINK         OD1BASP A 255                NI    NI A 392     1555   1555  2.16
LINK         OD2BASP A 255                NI    NI A 392     1555   1555  1.74
LINK         OD1 ASP A 257                NI    NI A 392     1555   1555  2.24
LINK         OD2 ASP A 287                NI    NI A 393     1555   1555  2.13
LINK        NI    NI A 391                 O1  GLO A 401     1555   1555  2.41
LINK        NI    NI A 391                 O2  GLO A 401     1555   1555  2.16
LINK        NI    NI A 391                 O   HOH A1001     1555   1555  1.78
LINK        NI    NI A 392                 O   HOH A1001     1555   1555  2.46
LINK        NI    NI A 393                 O4  GLO A 401     1555   1555  2.16
LINK        NI    NI A 393                 O2  GLO A 401     1555   1555  2.07
CISPEP   1 GLU A  186    PRO A  187          0         8.76
SITE     1 AC1  7 GLU A 217  HIS A 220  ASP A 255   NI A 392
SITE     2 AC1  7  NI A 393  GLO A 401  HOH A1001
SITE     1 AC2  7 GLU A 217  HIS A 220  ASP A 255  ASP A 257
SITE     2 AC2  7  NI A 391  GLO A 401  HOH A1001
SITE     1 AC3  6 GLU A 181  GLU A 217  ASP A 245  ASP A 287
SITE     2 AC3  6  NI A 391  GLO A 401
SITE     1 AC4 19 TRP A  16  PHE A  26  HIS A  54  THR A  90
SITE     2 AC4 19 VAL A 135  TRP A 137  GLU A 181  LYS A 183
SITE     3 AC4 19 GLU A 217  HIS A 220  ASP A 245  ASP A 255
SITE     4 AC4 19 ASP A 287   NI A 391   NI A 392   NI A 393
SITE     5 AC4 19 HOH A1001  HOH A1096  HOH A1111
CRYST1   94.007   99.669  102.862  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      0.010638  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010033  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009722        0.00000
      
PROCHECK
Go to PROCHECK summary
 References