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PDBsum entry 4a8l

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Isomerase PDB id
4a8l
Jmol
Contents
Protein chain
386 a.a.
Ligands
EDO
Metals
_CO ×2
Waters ×491
HEADER    ISOMERASE                               21-NOV-11   4A8L
TITLE     PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE CRYSTALS
TITLE    2 GROWN DURING THE PCDF-PROTEIN MISSION
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: XYLOSE ISOMERASE;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: D-XYLOSE KETOL ISOMERASE;
COMPND   5 EC: 5.3.1.5
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS;
SOURCE   3 ORGANISM_TAXID: 1929
KEYWDS    ISOMERASE, MICROGRAVITY
EXPDTA    X-RAY DIFFRACTION
AUTHOR    K.DECANNIERE,L.-D.PATINO-LOPEZ,M.SLEUTEL,C.EVRARD,C.VAN DE WEERDT,
AUTHOR   2 E.HAUMONT,J.A.GAVIRA,F.OTALORA,D.MAES
REVDAT   1   30-NOV-11 4A8L    0
JRNL        AUTH   K.DECANNIERE,L.-D.PATINO-LOPEZ,M.SLEUTEL,C.EVRARD,
JRNL        AUTH 2 C.VAN DE WEERDT,E.HAUMONT,J.A.GAVIRA,F.OTALORA,D.MAES
JRNL        TITL   PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE
JRNL        TITL 2 CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION
JRNL        REF    TO BE PUBLISHED
JRNL        REFN
REMARK   2
REMARK   2 RESOLUTION.    1.35 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : REFMAC 5.5.0110
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON
REMARK   3
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 70.87
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NONE
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.84
REMARK   3   NUMBER OF REFLECTIONS             : 96519
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.11142
REMARK   3   R VALUE            (WORKING SET) : 0.11007
REMARK   3   FREE R VALUE                     : 0.13676
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.0
REMARK   3   FREE R VALUE TEST SET COUNT      : 5124
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : 20
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.351
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.386
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 6951
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 98.49
REMARK   3   BIN R VALUE           (WORKING SET) : 0.076
REMARK   3   BIN FREE R VALUE SET COUNT          : 412
REMARK   3   BIN FREE R VALUE                    : 0.128
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 3218
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 6
REMARK   3   SOLVENT ATOMS            : 489
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 10.910
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : -0.02
REMARK   3    B22 (A**2) : 0.25
REMARK   3    B33 (A**2) : -0.23
REMARK   3    B12 (A**2) : 0.00
REMARK   3    B13 (A**2) : 0.00
REMARK   3    B23 (A**2) : 0.00
REMARK   3
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.
REMARK   3   ESU BASED ON R VALUE                            (A): 0.037
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.037
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.017
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.882
REMARK   3
REMARK   3  CORRELATION COEFFICIENTS.
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.976
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.967
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  3295 ; 0.025 ; 0.022
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  4507 ; 2.194 ; 1.957
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   439 ; 5.704 ; 5.000
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   175 ;33.409 ;23.086
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   524 ;11.094 ;15.000
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    36 ;16.007 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   467 ; 0.127 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2677 ; 0.016 ; 0.021
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  2027 ; 2.422 ; 1.500
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3257 ; 3.239 ; 2.000
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1268 ; 4.345 ; 3.000
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1231 ; 5.627 ; 4.500
REMARK   3
REMARK   3  ANISOTROPIC THERMAL FACTOR RESTRAINTS.   COUNT   RMS    WEIGHT
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  3295 ; 2.694 ; 3.000
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):   493 ;13.568 ; 3.000
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  3191 ; 6.561 ; 3.000
REMARK   3
REMARK   3  NCS RESTRAINTS STATISTICS
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : NULL
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED : BABINET MODEL WITH MASK
REMARK   3   PARAMETERS FOR MASK CALCULATION
REMARK   3   VDW PROBE RADIUS   : 1.40
REMARK   3   ION PROBE RADIUS   : 0.80
REMARK   3   SHRINKAGE RADIUS   : 0.80
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE
REMARK   3   RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
REMARK   4
REMARK   4 4A8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-11.
REMARK 100 THE PDBE ID CODE IS EBI-50390.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 10-SEP-09
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 7.0
REMARK 200  NUMBER OF CRYSTALS USED        : 13
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : ESRF
REMARK 200  BEAMLINE                       : BM16
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.977
REMARK 200  MONOCHROMATOR                  : DOUBLE CRYSTAL
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : ADSC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200  DATA SCALING SOFTWARE          : XDS
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 197146
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.35
REMARK 200  RESOLUTION RANGE LOW       (A) : 24.60
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.0
REMARK 200  DATA REDUNDANCY                : 46
REMARK 200  R MERGE                    (I) : 0.05
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 69.00
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.39
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 23
REMARK 200  R MERGE FOR SHELL          (I) : 0.13
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : 31.00
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: PDB ENTRY 2GLK
REMARK 200
REMARK 200 REMARK: STRUCTURE FACTOR FILE HAS DATA TILL 0.977 ANGSTROM.
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 54
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.7
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 32.7 MG/ML PROTEIN, 0.6 M
REMARK 280  AMMONIUM SULPHATE, 100 MM HEPES PH 7.0
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       46.28000
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       49.21000
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       51.06500
REMARK 290   SMTRY1   6 -1.000000  0.000000  0.000000       46.28000
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       49.21000
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000       51.06500
REMARK 290   SMTRY1   7 -1.000000  0.000000  0.000000       46.28000
REMARK 290   SMTRY2   7  0.000000  1.000000  0.000000       49.21000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       51.06500
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000       46.28000
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000       49.21000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       51.06500
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: 32210 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 46250 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -220.5 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        0.00000
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        0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     MET A     1
REMARK 465     GLY A   388
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470   M RES CSSEQI  ATOMS
REMARK 470     ASN A   2    CG   OD1  ND2
REMARK 470     GLU A   8    CG   CD   OE1  OE2
REMARK 470     ARG A  10    CD   NE   CZ   NH1  NH2
REMARK 470     ARG A  32    NE   CZ   NH1  NH2
REMARK 470     ARG A  41    NE   CZ   NH1  NH2
REMARK 470     GLU A 132    CG   CD   OE1  OE2
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   O    HOH A  2210     O    HOH A  2211              1.93
REMARK 500   OE2  GLU A   328     O    HOH A  2409              1.94
REMARK 500   O    HOH A  2009     O    HOH A  2011              2.17
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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   RES CSSEQI ATM2   DEVIATION
REMARK 500    ASP A  24   C     PRO A  25   N       0.194
REMARK 500    ARG A  76   CZ    ARG A  76   NH2    -0.086
REMARK 500    LYS A  85   CE    LYS A  85   NZ      0.206
REMARK 500    GLU A 128   CG    GLU A 128   CD      0.120
REMARK 500    GLU A 181   CD    GLU A 181   OE2     0.079
REMARK 500    GLU A 204   CD    GLU A 204   OE2     0.079
REMARK 500    ASP A 255   CB    ASP A 255   CG     -0.175
REMARK 500    ARG A 266   NE    ARG A 266   CZ      0.086
REMARK 500    ARG A 266   CZ    ARG A 266   NH2    -0.105
REMARK 500    PHE A 296   CD1   PHE A 296   CE1     0.130
REMARK 500    ARG A 340   CG    ARG A 340   CD      0.177
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    ASP A  81   CB  -  CG  -  OD1 ANGL. DEV. =   6.3 DEGREES
REMARK 500    ARG A 152   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.4 DEGREES
REMARK 500    ARG A 177   NE  -  CZ  -  NH1 ANGL. DEV. =  -3.8 DEGREES
REMARK 500    ARG A 177   NE  -  CZ  -  NH2 ANGL. DEV. =   3.7 DEGREES
REMARK 500    ARG A 188   NE  -  CZ  -  NH1 ANGL. DEV. =   3.8 DEGREES
REMARK 500    GLU A 217   OE1 -  CD  -  OE2 ANGL. DEV. =   7.3 DEGREES
REMARK 500    ASP A 255   OD1 -  CG  -  OD2 ANGL. DEV. = -15.1 DEGREES
REMARK 500    ASP A 255   CB  -  CG  -  OD1 ANGL. DEV. =  12.8 DEGREES
REMARK 500    ARG A 266   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.1 DEGREES
REMARK 500    PHE A 296   CB  -  CG  -  CD2 ANGL. DEV. =  -4.4 DEGREES
REMARK 500    GLU A 337   CG  -  CD  -  OE1 ANGL. DEV. =  13.8 DEGREES
REMARK 500    ARG A 374   NE  -  CZ  -  NH1 ANGL. DEV. =  -8.9 DEGREES
REMARK 500    ARG A 374   NE  -  CZ  -  NH2 ANGL. DEV. =   7.5 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      -75.29    -84.71
REMARK 500    PHE A  94      -25.48   -140.73
REMARK 500    ASP A 175       76.30   -108.11
REMARK 500    GLU A 186      100.75     83.67
REMARK 500    ASN A 247     -169.14   -167.83
REMARK 500    ALA A 343       61.74   -151.75
REMARK 500    PHE A 357      -75.12   -154.62
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500  M RES CSSEQI        ANGLE
REMARK 500    ASP A  24         15.45
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600 1,2-ETHANEDIOL (EDO): TENTATIVE
REMARK 600 COBALT (II) ION (CO): COBALT MOST LIKELY GIVEN ANOMALOUS
REMARK 600  EFFECT AT DIFFERENT WAVELENGTHS
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                              CO A1389  CO
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 181   OE2
REMARK 620 2 GLU A 217   OE1  97.3
REMARK 620 3 ASP A 245   OD2  91.9 104.8
REMARK 620 4 ASP A 287   OD2 161.0  87.1 104.9
REMARK 620 5 EDO A1388   O2   85.9 167.7  86.9  86.3
REMARK 620 6 HOH A2277   O    83.8  96.9 158.3  77.3  71.6
REMARK 620 N                    1     2     3     4     5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              CO A1390  CO
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 255   OD2
REMARK 620 2 ASP A 257   OD1  98.5
REMARK 620 3 HOH A2301   O    99.1  75.2
REMARK 620 4 GLU A 217   OE2 161.0  90.7  99.4
REMARK 620 5 ASP A 255   OD1  55.4  86.9 146.6 108.9
REMARK 620 N                    1     2     3     4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1388
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  CO A1389
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  CO A1390
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1GW9   RELATED DB: PDB
REMARK 900  TRI-IODIDE DERIVATIVE OF XYLOSE ISOMERASE FROM
REMARK 900  STREPTOMYCES RUBIGINOSUS
REMARK 900 RELATED ID: 1OAD   RELATED DB: PDB
REMARK 900  GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212
REMARK 900   CRYSTAL FORM
REMARK 900 RELATED ID: 1XIB   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE (PH 7.4)
REMARK 900 RELATED ID: 1XIJ   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH THREONATE AND MN (PH
REMARK 900   9.0)
REMARK 900 RELATED ID: 1XIE   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH 1,5-DIANHYDROSORBITOL
REMARK 900   (PH 7.4)
REMARK 900 RELATED ID: 4A8I   RELATED DB: PDB
REMARK 900  PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE
REMARK 900   CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION
REMARK 900 RELATED ID: 1XIC   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH D-XYLOSE (PH 9.0)
REMARK 900 RELATED ID: 3XIS   RELATED DB: PDB
REMARK 900  XYLOSE ISOMERASE COMPLEX WITH XYLOSE
REMARK 900 RELATED ID: 2GLK   RELATED DB: PDB
REMARK 900  HIGH-RESOLUTION STUDY OF D-XYLOSE ISOMERASE, 0.
REMARK 900  94ARESOLUTION.
REMARK 900 RELATED ID: 1MNZ   RELATED DB: PDB
REMARK 900  ATOMIC STRUCTURE OF GLUCOSE ISOMERASE
REMARK 900 RELATED ID: 1XII   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH 300MM D-XYLULOSE AND
REMARK 900   MN (PH 8.0)
REMARK 900 RELATED ID: 1XIF   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH GLUCOSE, MN, AND MG
REMARK 900   (PH 8.0)
REMARK 900 RELATED ID: 2XIS   RELATED DB: PDB
REMARK 900  XYLOSE ISOMERASE COMPLEX WITH XYLITOL
REMARK 900 RELATED ID: 1XIS   RELATED DB: PDB
REMARK 900  XYLOSE ISOMERASE COMPLEX WITH MNCL2
REMARK 900 RELATED ID: 9XIA   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEX WITH INACTIVATOR
REMARK 900 RELATED ID: 1XID   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH L-ASCORBIC ACID, MN
REMARK 900  , AND MG (PH 7.4)
REMARK 900 RELATED ID: 1O1H   RELATED DB: PDB
REMARK 900  STRUCTURE OF GLUCOSE ISOMERASE DERIVATIZED WITH KR.
REMARK 900 RELATED ID: 1XIG   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH XYLITOL, MG, AND MN
REMARK 900   (PH 7.4)
REMARK 900 RELATED ID: 2GVE   RELATED DB: PDB
REMARK 900  TIME-OF-FLIGHT NEUTRON DIFFRACTION STRUCTURE OF D-
REMARK 900  XYLOSEISOMERASE
REMARK 900 RELATED ID: 4XIS   RELATED DB: PDB
REMARK 900  XYLOSE ISOMERASE COMPLEX WITH XYLOSE AND MNCL2
REMARK 900 RELATED ID: 8XIA   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEX WITH D-XYLOSE
REMARK 900 RELATED ID: 2GUB   RELATED DB: PDB
REMARK 900  CRYSTAL STRUCTURE OF METAL FREE D-XYLOSE ISOMERASE.
REMARK 900 RELATED ID: 1XIH   RELATED DB: PDB
REMARK 900  D-XYLOSE ISOMERASE COMPLEXED WITH D-SORBITOL AND NO
REMARK 900  ADDED MN (PH 9.0)
REMARK 900 RELATED ID: 4A8R   RELATED DB: PDB
REMARK 900  PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE
REMARK 900   CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION
DBREF  4A8L 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    EDO  A1388       4
HET     CO  A1389       1
HET     CO  A1390       1
HETNAM     EDO 1,2-ETHANEDIOL
HETNAM      CO COBALT (II) ION
HETSYN     EDO ETHYLENE GLYCOL
FORMUL   2  EDO    C2 H6 O2
FORMUL   3   CO    2(CO 2+)
FORMUL   4  HOH   *489(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 ASP A  150  GLY A  173  1                                  24
HELIX    9   9 THR A  195  GLU A  204  1                                  10
HELIX   10  10 ARG A  208  GLU A  210  5                                   3
HELIX   11  11 GLU A  217  MET A  223  1                                   7
HELIX   12  12 ASN A  227  ALA A  238  1                                  12
HELIX   13  13 ASP A  264  GLY A  279  1                                  16
HELIX   14  14 ASP A  295  ASP A  323  1                                  29
HELIX   15  15 ASP A  323  SER A  333  1                                  11
HELIX   16  16 ARG A  334  ALA A  339  1                                   6
HELIX   17  17 GLY A  346  ASP A  352  1                                   7
HELIX   18  18 ASP A  353  PHE A  357  5                                   5
HELIX   19  19 ASP A  361  ARG A  368  1                                   8
HELIX   20  20 ALA A  371  GLY A  385  1                                  15
SHEET    1  AA 8 TYR A 212  VAL A 214  0
SHEET    2  AA 8 ARG A 177  ILE A 180  1  O  PHE A 178   N  GLY A 213
SHEET    3  AA 8 THR A 133  ALA A 136  1  O  TYR A 134   N  ALA A 179
SHEET    4  AA 8 MET A  88  THR A  90  1  O  ALA A  89   N  VAL A 135
SHEET    5  AA 8 GLY A  50  HIS A  54  1  O  PHE A  53   N  THR A  90
SHEET    6  AA 8 PHE A  11  GLY A  14  1  O  PHE A  13   N  THR A  52
SHEET    7  AA 8 ARG A 284  PHE A 286  1  O  ARG A 284   N  THR A  12
SHEET    8  AA 8 ASP A 245  LEU A 246  1  N  LEU A 246   O  HIS A 285
SHEET    1  AB 2 GLY A 142  ALA A 143  0
SHEET    2  AB 2 ASP A 190  ILE A 191 -1  O  ASP A 190   N  ALA A 143
LINK         C2  EDO A1388                CO    CO A1389     1555   1555  3.33
LINK         O2  EDO A1388                CO    CO A1389     1555   1555  2.36
LINK        CO    CO A1389                 OE2 GLU A 181     1555   1555  2.14
LINK        CO    CO A1389                 OE1 GLU A 217     1555   1555  2.10
LINK        CO    CO A1389                 OD2 ASP A 245     1555   1555  2.31
LINK        CO    CO A1389                 OD2 ASP A 287     1555   1555  2.11
LINK        CO    CO A1389                 O   HOH A2277     1555   1555  2.40
LINK        CO    CO A1390                 OD1 ASP A 257     1555   1555  2.50
LINK        CO    CO A1390                 O   HOH A2301     1555   1555  2.12
LINK        CO    CO A1390                 OE2 GLU A 217     1555   1555  2.04
LINK        CO    CO A1390                 OD1 ASP A 255     1555   1555  2.13
LINK        CO    CO A1390                 OD2 ASP A 255     1555   1555  2.35
CISPEP   1 GLU A  186    PRO A  187          0        20.09
SITE     1 AC1  9 HIS A  54  TRP A 137  GLU A 181  ASP A 245
SITE     2 AC1  9 ASP A 287   CO A1389  HOH A2160  HOH A2277
SITE     3 AC1  9 HOH A2331
SITE     1 AC2  6 GLU A 181  GLU A 217  ASP A 245  ASP A 287
SITE     2 AC2  6 EDO A1388  HOH A2277
SITE     1 AC3  5 GLU A 217  HIS A 220  ASP A 255  ASP A 257
SITE     2 AC3  5 HOH A2301
CRYST1   92.560   98.420  102.130  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      0.010804  0.000000  0.000000        0.00000
SCALE2      0.000000  0.010161  0.000000        0.00000
SCALE3      0.000000  0.000000  0.009791        0.00000
      
PROCHECK
Go to PROCHECK summary
 References