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PDBsum entry 1iov

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Ligase PDB id
1iov
Jmol
Contents
Protein chain
306 a.a.
Ligands
ADP
POB
Metals
_MG ×3
Waters ×263
HEADER    LIGASE                                  20-SEP-96   1IOV
TITLE     COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL
TITLE    2 PHOSPHONATE
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: D-ALA\:D-ALA LIGASE;
COMPND   3 CHAIN: A;
COMPND   4 EC: 6.3.2.4;
COMPND   5 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE   3 ORGANISM_TAXID: 562;
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   6 EXPRESSION_SYSTEM_GENE: DDLB;
SOURCE   7 OTHER_DETAILS: ENZYME PROVIDED BY C.T. WALSH, HARVARD MED
SOURCE   8 SCHOOL. SEE ZAWADZKE ET AL. BIOCHEM. 30, P. 1673, 1991.
KEYWDS    GLYCOGEN PHOSPHORYLASE, LIGASE, CELL WALL, PEPTIDOGLYCAN
KEYWDS   2 SYNTHESIS, VANCOMYCIN, ADP BINDING
EXPDTA    X-RAY DIFFRACTION
AUTHOR    J.R.KNOX,P.C.MOEWS,C.FAN
REVDAT   4   24-FEB-09 1IOV    1       VERSN
REVDAT   3   01-APR-03 1IOV    1       JRNL
REVDAT   2   30-NOV-99 1IOV    1       JRNL   HEADER
REVDAT   1   12-FEB-97 1IOV    0
JRNL        AUTH   C.FAN,I.S.PARK,C.T.WALSH,J.R.KNOX
JRNL        TITL   D-ALANINE:D-ALANINE LIGASE: PHOSPHONATE AND
JRNL        TITL 2 PHOSPHINATE INTERMEDIATES WITH WILD TYPE AND THE
JRNL        TITL 3 Y216F MUTANT.
JRNL        REF    BIOCHEMISTRY                  V.  36  2531 1997
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   9054558
JRNL        DOI    10.1021/BI962431T
REMARK   1
REMARK   1 REFERENCE 1
REMARK   1  AUTH   C.FAN,P.C.MOEWS,Y.SHI,C.T.WALSH,J.R.KNOX
REMARK   1  TITL   A COMMON FOLD FOR PEPTIDE SYNTHETASES CLEAVING ATP
REMARK   1  TITL 2 TO ADP
REMARK   1  REF    PROC.NATL.ACAD.SCI.USA        V.  92  1172 1995
REMARK   1  REFN                   ISSN 0027-8424
REMARK   1 REFERENCE 2
REMARK   1  AUTH   C.FAN,P.C.MOEWS,C.T.WALSH,J.R.KNOX
REMARK   1  TITL   VANCOMYCIN RESISTANCE: STRUCTURE OF
REMARK   1  TITL 2 D-ALANINE:D-ALANINE LIGASE AT 2.3 A RESOLUTION
REMARK   1  REF    SCIENCE                       V. 266   439 1994
REMARK   1  REFN                   ISSN 0036-8075
REMARK   2
REMARK   2 RESOLUTION.    2.20 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PROLSQ
REMARK   3   AUTHORS     : KONNERT,HENDRICKSON
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 15.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 3.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 75.0
REMARK   3   NUMBER OF REFLECTIONS             : 7591
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 + TEST SET) : NULL
REMARK   3   R VALUE            (WORKING SET) : 0.156
REMARK   3   FREE R VALUE                     : 0.204
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2293
REMARK   3   NUCLEIC ACID ATOMS       : 27
REMARK   3   HETEROGEN ATOMS          : 17
REMARK   3   SOLVENT ATOMS            : 263
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 10.30
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) : 0.20
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA
REMARK   3    BOND LENGTH                     (A) : 0.008 ; 0.020
REMARK   3    ANGLE DISTANCE                  (A) : 1.100 ; NULL
REMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) : 0.019 ; 0.040
REMARK   3    H-BOND OR METAL COORDINATION    (A) : NULL  ; NULL
REMARK   3
REMARK   3   PLANE RESTRAINT                  (A) : 0.005 ; 0.018
REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) : 0.115 ; 0.150
REMARK   3
REMARK   3   NON-BONDED CONTACT RESTRAINTS.
REMARK   3    SINGLE TORSION                  (A) : 0.204 ; 0.500
REMARK   3    MULTIPLE TORSION                (A) : 0.305 ; 0.500
REMARK   3    H-BOND (X...Y)                  (A) : 0.365 ; 0.500
REMARK   3    H-BOND (X-H...Y)                (A) : NULL  ; NULL
REMARK   3
REMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK   3    SPECIFIED                 (DEGREES) : NULL  ; NULL
REMARK   3    PLANAR                    (DEGREES) : 1.100 ; 3.000
REMARK   3    STAGGERED                 (DEGREES) : 22.500; 15.000
REMARK   3    TRANSVERSE                (DEGREES) : 19.600; 20.000
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND               (A**2) : 0.263 ; 1.000
REMARK   3   MAIN-CHAIN ANGLE              (A**2) : 0.472 ; 1.500
REMARK   3   SIDE-CHAIN BOND               (A**2) : 0.197 ; 1.000
REMARK   3   SIDE-CHAIN ANGLE              (A**2) : 0.356 ; 1.500
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1IOV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 1995
REMARK 200  TEMPERATURE           (KELVIN) : 295
REMARK 200  PH                             : 6.5
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 RUH2R
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : AREA DETECTOR
REMARK 200  DETECTOR MANUFACTURER          : SIEMENS
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XENGEN
REMARK 200  DATA SCALING SOFTWARE          : XENGEN
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 11579
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.200
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 75.0
REMARK 200  DATA REDUNDANCY                : NULL
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.06700
REMARK 200   FOR THE DATA SET  : 8.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.40
REMARK 200  COMPLETENESS FOR SHELL     (%) : 39.0
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: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PROLSQ
REMARK 200 STARTING MODEL: 2DLN
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 37.17
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 6.5
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z
REMARK 290       4555   X+1/2,-Y+1/2,-Z
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       49.30000
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       25.50000
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       49.30000
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       25.50000
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000
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: MONOMERIC
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 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   NH1  ARG A    31     O    ALA A    37              2.10
REMARK 500   OE2  GLU A   187     O3'  ADP A   310              2.11
REMARK 500   O    MET A     1     N    ASP A     3              2.12
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE
REMARK 500   O    HOH A   489     O    HOH A   506     1554     1.13
REMARK 500   O    HOH A   456     O    HOH A   456     2565     1.16
REMARK 500   O    HOH A   494     O    HOH A   494     2565     1.24
REMARK 500   O    HOH A   468     O    HOH A   579     3546     1.27
REMARK 500   O    HOH A   413     O    HOH A   653     2555     1.28
REMARK 500   O    HOH A   426     O    HOH A   654     1565     1.29
REMARK 500   CB   SER A   155     O    HOH A   437     3547     1.47
REMARK 500   O    HOH A   474     O    HOH A   594     2555     1.47
REMARK 500   O    HOH A   504     O    HOH A   663     3556     1.51
REMARK 500   O    HOH A   473     O    HOH A   475     2555     1.68
REMARK 500   O    HOH A   486     O    HOH A   650     3556     1.74
REMARK 500   O    HOH A   574     O    HOH A   593     2555     1.83
REMARK 500   O    HOH A   533     O    HOH A   565     3557     1.84
REMARK 500   O    HOH A   532     O    HOH A   614     3557     1.85
REMARK 500   OH   TYR A   212     NH1  ARG A   288     3547     1.85
REMARK 500   O    HOH A   499     O    HOH A   499     2565     1.86
REMARK 500   O    ALA A   227     O    HOH A   492     3556     1.89
REMARK 500   O    HOH A   446     O    HOH A   662     1565     1.94
REMARK 500   O    HOH A   594     O    HOH A   651     2555     2.00
REMARK 500   CG   GLN A   204     O    HOH A   609     3556     2.01
REMARK 500   NZ   LYS A   156     OE2  GLU A   230     3546     2.03
REMARK 500   O    HOH A   578     O    HOH A   586     1565     2.08
REMARK 500   O    HOH A   495     O    HOH A   496     2565     2.10
REMARK 500   O    HOH A   587     O    HOH A   588     2565     2.11
REMARK 500   O    HOH A   559     O    HOH A   569     3547     2.13
REMARK 500   OE1  GLU A    17     O    HOH A   652     3557     2.14
REMARK 500   O    HOH A   631     O    HOH A   638     3547     2.15
REMARK 500   CD   LYS A     4     O    HOH A   570     1556     2.17
REMARK 500   OE2  GLU A    17     O    HOH A   652     3557     2.17
REMARK 500   OE2  GLU A   148     O    HOH A   420     3547     2.18
REMARK 500   O    HOH A   458     O    HOH A   637     3556     2.18
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    ARG A  16   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 DEGREES
REMARK 500    ARG A  16   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.2 DEGREES
REMARK 500    ASP A  41   CB  -  CG  -  OD2 ANGL. DEV. =   6.6 DEGREES
REMARK 500    ARG A  65   NE  -  CZ  -  NH1 ANGL. DEV. =   5.4 DEGREES
REMARK 500    ARG A  65   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.3 DEGREES
REMARK 500    ASP A  96   CB  -  CG  -  OD1 ANGL. DEV. =   5.6 DEGREES
REMARK 500    ARG A  99   NE  -  CZ  -  NH1 ANGL. DEV. =   4.2 DEGREES
REMARK 500    LEU A 178   CA  -  CB  -  CG  ANGL. DEV. =  20.1 DEGREES
REMARK 500    TYR A 210   CB  -  CG  -  CD2 ANGL. DEV. =  -4.4 DEGREES
REMARK 500    TYR A 210   CB  -  CG  -  CD1 ANGL. DEV. =   3.9 DEGREES
REMARK 500    ARG A 255   NE  -  CZ  -  NH1 ANGL. DEV. =   3.5 DEGREES
REMARK 500    ARG A 255   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.3 DEGREES
REMARK 500    ASP A 263   CB  -  CG  -  OD1 ANGL. DEV. =   6.2 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   2      -54.43     65.94
REMARK 500    GLU A  44      -75.04   -149.19
REMARK 500    THR A  71      -73.55    -54.84
REMARK 500    SER A  86      134.80    -29.45
REMARK 500    ALA A 159      136.48    100.99
REMARK 500    SER A 184       76.31   -101.57
REMARK 500    LEU A 217       68.73   -118.88
REMARK 500    PRO A 226     -168.66    -67.15
REMARK 500    ALA A 231       11.41    -61.33
REMARK 500    SER A 232      -60.43   -101.88
REMARK 500    LEU A 237      -70.97    -61.86
REMARK 500    GLU A 270     -177.94   -171.09
REMARK 500    SER A 274       67.85   -153.32
REMARK 500    MET A 277       36.83   -147.16
REMARK 500    ALA A 290       20.63    -76.70
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  31         0.12    SIDE_CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525  M RES CSSEQI
REMARK 525    HOH A 408        DISTANCE =  7.45 ANGSTROMS
REMARK 525    HOH A 418        DISTANCE =  5.97 ANGSTROMS
REMARK 525    HOH A 428        DISTANCE =  7.13 ANGSTROMS
REMARK 525    HOH A 435        DISTANCE =  7.30 ANGSTROMS
REMARK 525    HOH A 437        DISTANCE =  6.82 ANGSTROMS
REMARK 525    HOH A 439        DISTANCE =  9.31 ANGSTROMS
REMARK 525    HOH A 456        DISTANCE =  5.24 ANGSTROMS
REMARK 525    HOH A 460        DISTANCE =  5.10 ANGSTROMS
REMARK 525    HOH A 465        DISTANCE = 10.66 ANGSTROMS
REMARK 525    HOH A 467        DISTANCE =  9.12 ANGSTROMS
REMARK 525    HOH A 468        DISTANCE =  9.79 ANGSTROMS
REMARK 525    HOH A 472        DISTANCE =  5.50 ANGSTROMS
REMARK 525    HOH A 473        DISTANCE =  5.18 ANGSTROMS
REMARK 525    HOH A 492        DISTANCE =  6.19 ANGSTROMS
REMARK 525    HOH A 497        DISTANCE =  5.15 ANGSTROMS
REMARK 525    HOH A 498        DISTANCE = 12.17 ANGSTROMS
REMARK 525    HOH A 500        DISTANCE =  9.52 ANGSTROMS
REMARK 525    HOH A 503        DISTANCE = 13.71 ANGSTROMS
REMARK 525    HOH A 533        DISTANCE =  6.60 ANGSTROMS
REMARK 525    HOH A 552        DISTANCE =  8.02 ANGSTROMS
REMARK 525    HOH A 554        DISTANCE =  8.52 ANGSTROMS
REMARK 525    HOH A 558        DISTANCE =  5.40 ANGSTROMS
REMARK 525    HOH A 586        DISTANCE =  5.21 ANGSTROMS
REMARK 525    HOH A 587        DISTANCE = 10.07 ANGSTROMS
REMARK 525    HOH A 588        DISTANCE =  6.82 ANGSTROMS
REMARK 525    HOH A 603        DISTANCE =  6.06 ANGSTROMS
REMARK 525    HOH A 607        DISTANCE =  7.21 ANGSTROMS
REMARK 525    HOH A 612        DISTANCE =  6.97 ANGSTROMS
REMARK 525    HOH A 613        DISTANCE = 10.62 ANGSTROMS
REMARK 525    HOH A 622        DISTANCE =  5.21 ANGSTROMS
REMARK 525    HOH A 626        DISTANCE =  7.58 ANGSTROMS
REMARK 525    HOH A 630        DISTANCE =  9.26 ANGSTROMS
REMARK 525    HOH A 644        DISTANCE =  6.79 ANGSTROMS
REMARK 525    HOH A 646        DISTANCE =  5.28 ANGSTROMS
REMARK 525    HOH A 647        DISTANCE =  5.10 ANGSTROMS
REMARK 525    HOH A 654        DISTANCE =  7.22 ANGSTROMS
REMARK 525    HOH A 655        DISTANCE =  5.28 ANGSTROMS
REMARK 525    HOH A 656        DISTANCE =  8.35 ANGSTROMS
REMARK 525    HOH A 662        DISTANCE =  5.89 ANGSTROMS
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                              MG A 331  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ADP A 310   O2B
REMARK 620 2 POB A 321   O5P 101.4
REMARK 620 3 GLU A 270   OE2  78.8 102.8
REMARK 620 4 ASN A 272   OD1 174.7  82.0  96.5
REMARK 620 5 ADP A 310   O3B  50.8  66.9  55.2 128.3
REMARK 620 6 HOH A 536   O   114.1  76.1 167.0  70.6 133.1
REMARK 620 7 GLU A 270   OE1  98.2 142.2  50.1  76.7 103.2 123.7
REMARK 620 N                    1     2     3     4     5     6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A 330  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ADP A 310   O3B
REMARK 620 2 ADP A 310   O2A  81.9
REMARK 620 3 POB A 321   O4P  59.8 138.6
REMARK 620 4 ASP A 257   OD2 137.2  87.4 109.5
REMARK 620 5 GLU A 270   OE2  54.3  70.4  74.4  83.1
REMARK 620 N                    1     2     3     4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              MG A 332  MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 271   O
REMARK 620 2 HOH A 522   O   143.0
REMARK 620 3 SER A  94   O    91.2  85.1
REMARK 620 N                    1     2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ADP
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: ADP BINDING SITE.
REMARK 800 SITE_IDENTIFIER: LIG
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: LIGAND BINDING SITE.
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 330
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 331
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 332
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 310
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POB A 321
DBREF  1IOV A    2   306  UNP    P07862   DDLB_ECOLI       1    305
SEQRES   1 A  306  MET THR ASP LYS ILE ALA VAL LEU LEU GLY GLY THR SER
SEQRES   2 A  306  ALA GLU ARG GLU VAL SER LEU ASN SER GLY ALA ALA VAL
SEQRES   3 A  306  LEU ALA GLY LEU ARG GLU GLY GLY ILE ASP ALA TYR PRO
SEQRES   4 A  306  VAL ASP PRO LYS GLU VAL ASP VAL THR GLN LEU LYS SER
SEQRES   5 A  306  MET GLY PHE GLN LYS VAL PHE ILE ALA LEU HIS GLY ARG
SEQRES   6 A  306  GLY GLY GLU ASP GLY THR LEU GLN GLY MET LEU GLU LEU
SEQRES   7 A  306  MET GLY LEU PRO TYR THR GLY SER GLY VAL MET ALA SER
SEQRES   8 A  306  ALA LEU SER MET ASP LYS LEU ARG SER LYS LEU LEU TRP
SEQRES   9 A  306  GLN GLY ALA GLY LEU PRO VAL ALA PRO TRP VAL ALA LEU
SEQRES  10 A  306  THR ARG ALA GLU PHE GLU LYS GLY LEU SER ASP LYS GLN
SEQRES  11 A  306  LEU ALA GLU ILE SER ALA LEU GLY LEU PRO VAL ILE VAL
SEQRES  12 A  306  LYS PRO SER ARG GLU GLY SER SER VAL GLY MET SER LYS
SEQRES  13 A  306  VAL VAL ALA GLU ASN ALA LEU GLN ASP ALA LEU ARG LEU
SEQRES  14 A  306  ALA PHE GLN HIS ASP GLU GLU VAL LEU ILE GLU LYS TRP
SEQRES  15 A  306  LEU SER GLY PRO GLU PHE THR VAL ALA ILE LEU GLY GLU
SEQRES  16 A  306  GLU ILE LEU PRO SER ILE ARG ILE GLN PRO SER GLY THR
SEQRES  17 A  306  PHE TYR ASP TYR GLU ALA LYS TYR LEU SER ASP GLU THR
SEQRES  18 A  306  GLN TYR PHE CYS PRO ALA GLY LEU GLU ALA SER GLN GLU
SEQRES  19 A  306  ALA ASN LEU GLN ALA LEU VAL LEU LYS ALA TRP THR THR
SEQRES  20 A  306  LEU GLY CYS LYS GLY TRP GLY ARG ILE ASP VAL MET LEU
SEQRES  21 A  306  ASP SER ASP GLY GLN PHE TYR LEU LEU GLU ALA ASN THR
SEQRES  22 A  306  SER PRO GLY MET THR SER HIS SER LEU VAL PRO MET ALA
SEQRES  23 A  306  ALA ARG GLN ALA GLY MET SER PHE SER GLN LEU VAL VAL
SEQRES  24 A  306  ARG ILE LEU GLU LEU ALA ASP
HET     MG  A 330       1
HET     MG  A 331       1
HET     MG  A 332       1
HET    ADP  A 310      27
HET    POB  A 321      17
HETNAM      MG MAGNESIUM ION
HETNAM     ADP ADENOSINE-5'-DIPHOSPHATE
HETNAM     POB 2-[(1-AMINO-ETHYL)-PHOSPHATE-PHOSPHINOYLOXY]-BUTYRIC
HETNAM   2 POB  ACID
FORMUL   2   MG    3(MG 2+)
FORMUL   5  ADP    C10 H15 N5 O10 P2
FORMUL   6  POB    C6 H15 N O8 P2
FORMUL   7  HOH   *263(H2 O)
HELIX    1   1 ARG A   16  GLU A   32  1                                  17
HELIX    2   2 THR A   71  MET A   79  1                                   9
HELIX    3   3 VAL A   88  SER A   94  1                                   7
HELIX    4   4 LYS A   97  GLY A  106  1                                  10
HELIX    5   5 ARG A  119  PHE A  122  1                                   4
HELIX    6   6 LEU A  131  ALA A  136  1                                   6
HELIX    7   7 GLU A  160  GLN A  172  5                                  13
HELIX    8   8 TYR A  212  TYR A  216  1                                   5
HELIX    9   9 GLN A  233  THR A  246  1                                  14
HELIX   10  10 LEU A  282  GLN A  289  1                                   8
HELIX   11  11 PHE A  294  LEU A  302  1                                   9
SHEET    1   A 3 ASP A  36  ASP A  41  0
SHEET    2   A 3 LYS A   4  LEU A   9  1  N  ILE A   5   O  ASP A  36
SHEET    3   A 3 PHE A  55  ALA A  61  1  N  GLN A  56   O  LYS A   4
SHEET    1   B 4 TRP A 114  THR A 118  0
SHEET    2   B 4 GLU A 176  LYS A 181 -1  N  ILE A 179   O  VAL A 115
SHEET    3   B 4 VAL A 141  PRO A 145 -1  N  LYS A 144   O  LEU A 178
SHEET    4   B 4 SER A 155  VAL A 157 -1  N  VAL A 157   O  VAL A 141
SHEET    1   C 5 PHE A 266  ASN A 272  0
SHEET    2   C 5 TRP A 253  LEU A 260 -1  N  MET A 259   O  TYR A 267
SHEET    3   C 5 GLU A 187  LEU A 193 -1  N  ILE A 192   O  GLY A 254
SHEET    4   C 5 ILE A 201  GLN A 204 -1  N  ILE A 203   O  GLU A 187
SHEET    5   C 5 GLN A 222  PHE A 224 -1  N  PHE A 224   O  ARG A 202
LINK         O2B ADP A 310                MG    MG A 331     1555   1555  2.39
LINK         O3B ADP A 310                MG    MG A 330     1555   1555  2.40
LINK         O2A ADP A 310                MG    MG A 330     1555   1555  2.10
LINK         O4P POB A 321                MG    MG A 330     1555   1555  1.97
LINK         O5P POB A 321                MG    MG A 331     1555   1555  2.17
LINK        MG    MG A 330                 OD2 ASP A 257     1555   1555  1.94
LINK        MG    MG A 331                 OE2 GLU A 270     1555   1555  2.09
LINK        MG    MG A 331                 OD1 ASN A 272     1555   1555  2.32
LINK        MG    MG A 332                 O   ALA A 271     1555   1555  2.28
LINK        MG    MG A 330                 OE2 GLU A 270     1555   1555  2.84
LINK        MG    MG A 331                 O3B ADP A 310     1555   1555  2.90
LINK        MG    MG A 331                 O   HOH A 536     1555   1555  2.94
LINK        MG    MG A 331                 OE1 GLU A 270     1555   1555  2.76
LINK        MG    MG A 332                 O   HOH A 522     1555   1555  3.09
LINK        MG    MG A 332                 O   SER A  94     1555   1555  2.55
CISPEP   1 LEU A  139    PRO A  140          0        -1.35
CISPEP   2 CYS A  225    PRO A  226          0        -1.23
SITE     1 ADP 12 LYS A  97  LYS A 144  LYS A 215  GLU A 270
SITE     2 ADP 12 ASN A 272  SER A 151  GLU A 180  GLU A 187
SITE     3 ADP 12 TRP A 182  ALA A 159  ILE A 142  PHE A 209
SITE     1 LIG  6 GLU A  15  SER A 150  TYR A 216  VAL A  18
SITE     2 LIG  6 HIS A  63  SER A 281
SITE     1 AC1  4 ASP A 257  GLU A 270  ADP A 310  POB A 321
SITE     1 AC2  6 GLY A 149  GLU A 270  ASN A 272  ADP A 310
SITE     2 AC2  6 POB A 321  HOH A 536
SITE     1 AC3  4 SER A  94  GLU A 270  ALA A 271  HOH A 522
SITE     1 AC4 23 LYS A  97  ILE A 142  LYS A 144  GLU A 148
SITE     2 AC4 23 GLY A 149  SER A 150  SER A 151  MET A 154
SITE     3 AC4 23 GLU A 180  LYS A 181  TRP A 182  LEU A 183
SITE     4 AC4 23 GLU A 187  TYR A 210  LYS A 215  ASP A 257
SITE     5 AC4 23 MET A 259  LEU A 269  GLU A 270  POB A 321
SITE     6 AC4 23  MG A 330   MG A 331  HOH A 511
SITE     1 AC5 20 GLU A  15  GLY A 149  SER A 150  TYR A 210
SITE     2 AC5 20 LYS A 215  TYR A 216  ARG A 255  ASP A 257
SITE     3 AC5 20 GLU A 270  ASN A 272  PRO A 275  GLY A 276
SITE     4 AC5 20 SER A 281  LEU A 282  ADP A 310   MG A 330
SITE     5 AC5 20  MG A 331  HOH A 508  HOH A 536  HOH A 538
CRYST1   98.600   51.000   51.200  90.00  90.00  90.00 P 21 21 2     4
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      0.010142  0.000000  0.000000        0.00000
SCALE2      0.000000  0.019608  0.000000        0.00000
SCALE3      0.000000  0.000000  0.019531        0.00000
      
PROCHECK
Go to PROCHECK summary
 References