HEADER LIGASE 20-SEP-96 1IOV TITLE COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL 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 SCHOOL. SOURCE 8 SEE ZAWADZKE ET AL. BIOCHEM. 30, P. 1673, 1991. KEYWDS GLYCOGEN PHOSPHORYLASE, LIGASE, CELL WALL, PEPTIDOGLYCAN SYNTHESIS, KEYWDS 2 VANCOMYCIN, ADP BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.R.KNOX,P.C.MOEWS,C.FAN REVDAT 6 22-MAY-24 1IOV 1 REMARK REVDAT 5 09-AUG-23 1IOV 1 REMARK LINK 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 PHOSPHINATE JRNL TITL 2 INTERMEDIATES WITH WILD TYPE AND THE 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 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 D-ALANINE:D-ALANINE REMARK 1 TITL 2 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 : 2305 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 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. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174226. 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 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 332 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 94 O REMARK 620 2 ALA A 271 O 91.2 REMARK 620 3 HOH A 522 O 85.1 143.0 REMARK 620 N 1 2 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 ASP A 257 OD2 REMARK 620 2 GLU A 270 OE2 83.1 REMARK 620 3 ADP A 310 O3B 137.2 54.3 REMARK 620 4 ADP A 310 O2A 87.4 70.4 81.9 REMARK 620 5 POB A 321 O4P 109.5 74.4 59.8 138.6 REMARK 620 N 1 2 3 4 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 GLU A 270 OE2 REMARK 620 2 GLU A 270 OE1 50.1 REMARK 620 3 ASN A 272 OD1 96.5 76.7 REMARK 620 4 ADP A 310 O2B 78.8 98.2 174.7 REMARK 620 5 ADP A 310 O3B 55.2 103.2 128.3 50.8 REMARK 620 6 POB A 321 O5P 102.8 142.2 82.0 101.4 66.9 REMARK 620 7 HOH A 536 O 167.0 123.7 70.6 114.1 133.1 76.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ADP REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ADP BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: LIG REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: LIGAND BINDING SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 330 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 331 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 310 REMARK 800 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 O SER A 94 MG MG A 332 1555 1555 2.55 LINK OD2 ASP A 257 MG MG A 330 1555 1555 1.94 LINK OE2 GLU A 270 MG MG A 330 1555 1555 2.84 LINK OE2 GLU A 270 MG MG A 331 1555 1555 2.09 LINK OE1 GLU A 270 MG MG A 331 1555 1555 2.76 LINK O ALA A 271 MG MG A 332 1555 1555 2.28 LINK OD1 ASN A 272 MG MG A 331 1555 1555 2.32 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 O2B ADP A 310 MG MG A 331 1555 1555 2.39 LINK O3B ADP A 310 MG MG A 331 1555 1555 2.90 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 331 O HOH A 536 1555 1555 2.94 LINK MG MG A 332 O HOH A 522 1555 1555 3.09 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