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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
