HEADER TOXIN/ISOMERASE 27-NOV-09 3KUA OBSLTE 30-MAY-12 3KUA 4ELZ TITLE CCDBVFI:GYRA14VFI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA GYRASE (TYPE II TOPOISOMERASE), SUBUNIT A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 362-493; COMPND 5 SYNONYM: GYRA14; COMPND 6 EC: 5.99.1.3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CCDB; COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO FISCHERI; SOURCE 3 ORGANISM_TAXID: 312309; SOURCE 4 STRAIN: ATCC 700601 / ES114; SOURCE 5 GENE: GYRASE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: VIBRIO FISCHERI; SOURCE 13 ORGANISM_TAXID: 668; SOURCE 14 GENE: CCDB; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: B462; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PKK223-3 KEYWDS ALPHA+BETA, SH3 DOMAIN, TOPOISOMERASE, TOXIN-ISOMERASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.DE JONGE,R.LORIS,L.BUTS REVDAT 2 30-MAY-12 3KUA 1 OBSLTE VERSN REVDAT 1 17-NOV-10 3KUA 0 JRNL AUTH N.DE JONGE,M.SIMIC,L.BUTS,S.HAESAERTS,N.MINE,K.ROELANTS, JRNL AUTH 2 H.DE GREVE,L.VAN MELDEREN,J.LAH,R.LORIS JRNL TITL DISTINCT MECHANISMS OF GYRASE POISONING WITHIN THE CCDB JRNL TITL 2 FAMILY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 16.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 29888 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1652 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 16.9397 - 4.8437 1.00 2912 163 0.1918 0.2377 REMARK 3 2 4.8437 - 3.8596 1.00 2803 139 0.1537 0.1950 REMARK 3 3 3.8596 - 3.3761 0.99 2757 151 0.1760 0.2001 REMARK 3 4 3.3761 - 3.0694 0.98 2700 145 0.1902 0.2816 REMARK 3 5 3.0694 - 2.8505 0.94 2590 136 0.2023 0.2647 REMARK 3 6 2.8505 - 2.6832 0.93 2532 143 0.2010 0.3014 REMARK 3 7 2.6832 - 2.5492 0.93 2545 136 0.2055 0.2530 REMARK 3 8 2.5492 - 2.4386 0.93 2544 135 0.2044 0.2492 REMARK 3 9 2.4386 - 2.3450 0.94 2575 135 0.2110 0.2924 REMARK 3 10 2.3450 - 2.2643 0.94 2541 149 0.2202 0.3226 REMARK 3 11 2.2643 - 2.1936 0.96 2614 119 0.2367 0.2773 REMARK 3 12 2.1936 - 2.1310 0.76 2054 101 0.2331 0.3516 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.42 REMARK 3 B_SOL : 76.42 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.720 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.84 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.64700 REMARK 3 B22 (A**2) : -0.03800 REMARK 3 B33 (A**2) : -1.60800 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 3726 REMARK 3 ANGLE : 1.426 5069 REMARK 3 CHIRALITY : 0.098 613 REMARK 3 PLANARITY : 0.006 645 REMARK 3 DIHEDRAL : 16.638 1342 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (chain A) REMARK 3 ORIGIN FOR THE GROUP (A): 25.0192 -29.5533 -47.1065 REMARK 3 T TENSOR REMARK 3 T11: 0.0917 T22: 0.1407 REMARK 3 T33: 0.1103 T12: -0.0272 REMARK 3 T13: 0.0141 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.9585 L22: 2.5251 REMARK 3 L33: 0.7541 L12: -1.0986 REMARK 3 L13: 0.7593 L23: -0.9874 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: 0.0700 S13: -0.0930 REMARK 3 S21: 0.0647 S22: -0.0679 S23: -0.0969 REMARK 3 S31: -0.0744 S32: 0.0816 S33: 0.0317 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (chain B) REMARK 3 ORIGIN FOR THE GROUP (A): 5.6721 -1.6991 -48.4241 REMARK 3 T TENSOR REMARK 3 T11: 0.2094 T22: 0.1510 REMARK 3 T33: 0.2261 T12: -0.0156 REMARK 3 T13: -0.0182 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 1.2074 L22: 2.0238 REMARK 3 L33: 0.9344 L12: -0.9007 REMARK 3 L13: -0.4726 L23: 0.6210 REMARK 3 S TENSOR REMARK 3 S11: 0.0637 S12: 0.0722 S13: 0.2834 REMARK 3 S21: -0.0591 S22: -0.0951 S23: 0.0602 REMARK 3 S31: -0.2260 S32: -0.0197 S33: 0.0152 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (chain C) REMARK 3 ORIGIN FOR THE GROUP (A): 6.4136 -23.6882 -26.7928 REMARK 3 T TENSOR REMARK 3 T11: 0.2043 T22: 0.2044 REMARK 3 T33: 0.1536 T12: -0.0599 REMARK 3 T13: 0.0262 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.1037 L22: 2.9765 REMARK 3 L33: 0.9537 L12: 0.5482 REMARK 3 L13: 0.4093 L23: -1.0090 REMARK 3 S TENSOR REMARK 3 S11: -0.1357 S12: -0.0442 S13: -0.1040 REMARK 3 S21: 0.0485 S22: 0.1516 S23: 0.0192 REMARK 3 S31: 0.0286 S32: -0.2305 S33: -0.0177 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (chain D) REMARK 3 ORIGIN FOR THE GROUP (A): 20.6760 -7.8946 -26.0941 REMARK 3 T TENSOR REMARK 3 T11: 0.1682 T22: 0.2115 REMARK 3 T33: 0.2075 T12: -0.0511 REMARK 3 T13: -0.0646 T23: -0.0158 REMARK 3 L TENSOR REMARK 3 L11: 1.1408 L22: 3.6802 REMARK 3 L33: 1.2182 L12: 0.0044 REMARK 3 L13: -0.2212 L23: -0.2580 REMARK 3 S TENSOR REMARK 3 S11: -0.1258 S12: -0.0691 S13: 0.1108 REMARK 3 S21: 0.2141 S22: 0.0252 S23: -0.2796 REMARK 3 S31: -0.0544 S32: 0.0162 S33: 0.0783 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-DEC-09. REMARK 100 THE RCSB ID CODE IS RCSB056455. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8423 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29888 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.131 REMARK 200 RESOLUTION RANGE LOW (A) : 16.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 44.600 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : 0.15600 REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 44.60 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : 0.76000 REMARK 200 FOR SHELL : 3.112 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3KU8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M NAH2PO4, 0.8M K2HPO4, 100MM CAPS REMARK 280 PH10.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 26.75250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.25100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.25100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.75250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.29500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 342 REMARK 465 GLY A 343 REMARK 465 SER A 344 REMARK 465 SER A 345 REMARK 465 HIS A 346 REMARK 465 HIS A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 REMARK 465 HIS A 350 REMARK 465 HIS A 351 REMARK 465 MET B 342 REMARK 465 GLY B 343 REMARK 465 SER B 344 REMARK 465 SER B 345 REMARK 465 HIS B 346 REMARK 465 HIS B 347 REMARK 465 HIS B 348 REMARK 465 HIS B 349 REMARK 465 HIS B 350 REMARK 465 HIS B 351 REMARK 465 SER B 352 REMARK 465 SER B 353 REMARK 465 GLY B 354 REMARK 465 LEU B 355 REMARK 465 VAL B 356 REMARK 465 PRO B 357 REMARK 465 ARG B 358 REMARK 465 GLY B 359 REMARK 465 SER B 360 REMARK 465 HIS B 361 REMARK 465 ALA B 493 REMARK 465 SER B 494 REMARK 465 MET C 1 REMARK 465 MET D 1 REMARK 465 ASP D 47 REMARK 465 LYS D 48 REMARK 465 ILE D 105 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 ARG A 358 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 364 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 365 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 369 OE1 OE2 REMARK 470 LYS A 372 CD CE NZ REMARK 470 ARG A 426 NE CZ NH1 NH2 REMARK 470 ASP A 430 CG OD1 OD2 REMARK 470 GLU A 440 CG CD OE1 OE2 REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 GLU A 472 CG CD OE1 OE2 REMARK 470 GLU A 477 CD OE1 OE2 REMARK 470 GLU A 484 CG CD OE1 OE2 REMARK 470 MET B 362 CG SD CE REMARK 470 ARG B 364 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 365 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 372 CD CE NZ REMARK 470 GLU B 408 OE1 REMARK 470 ASN B 419 CB CG OD1 ND2 REMARK 470 GLU B 425 CD OE1 OE2 REMARK 470 ARG B 426 NE CZ NH1 NH2 REMARK 470 ASP B 430 CG OD1 OD2 REMARK 470 GLU B 440 OE1 OE2 REMARK 470 GLU B 445 CG CD OE1 OE2 REMARK 470 GLN B 453 OE1 NE2 REMARK 470 GLU B 484 CD OE1 OE2 REMARK 470 GLU B 487 CD OE1 OE2 REMARK 470 LYS C 10 CE NZ REMARK 470 LYS C 12 CG CD CE NZ REMARK 470 LYS C 16 NZ REMARK 470 ASP C 30 CG OD1 OD2 REMARK 470 GLU C 44 CG CD OE1 OE2 REMARK 470 LEU C 46 CG CD1 CD2 REMARK 470 ASP C 47 CG OD1 OD2 REMARK 470 LYS C 48 CG CD CE NZ REMARK 470 LYS C 49 CG CD CE NZ REMARK 470 LYS C 78 CE NZ REMARK 470 ILE C 105 CG1 CG2 CD1 REMARK 470 LYS D 8 CE NZ REMARK 470 LYS D 10 CD CE NZ REMARK 470 LYS D 12 CB CG CD CE NZ REMARK 470 LYS D 16 CG CD CE NZ REMARK 470 GLU D 44 CG CD OE1 OE2 REMARK 470 LEU D 45 CG CD1 CD2 REMARK 470 LYS D 49 CG CD CE NZ REMARK 470 ASP D 61 CG OD1 OD2 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 SER A 360 143.48 102.96 REMARK 500 ILE C 102 -68.44 -101.50 REMARK 500 LEU D 45 -6.32 -58.08 REMARK 500 PRO D 51 -14.46 -43.55 REMARK 500 SER D 52 -63.52 86.90 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 D 138 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH D 159 DISTANCE = 5.53 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KU8 RELATED DB: PDB REMARK 900 CCDBVFI:GYRA14EC REMARK 900 RELATED ID: 3JSC RELATED DB: PDB REMARK 900 CCDBVFI-FORMI-PH7.0 REMARK 900 RELATED ID: 3JRZ RELATED DB: PDB REMARK 900 CCDBVFI-FORMII-PH5.6 DBREF 3KUA A 363 494 UNP Q5E5J7 Q5E5J7_VIBF1 362 493 DBREF 3KUA B 363 494 UNP Q5E5J7 Q5E5J7_VIBF1 362 493 DBREF 3KUA C 1 105 UNP Q84B82 Q84B82_VIBFI 1 105 DBREF 3KUA D 1 105 UNP Q84B82 Q84B82_VIBFI 1 105 SEQADV 3KUA MET A 342 UNP Q5E5J7 INITIATING METHIONINE SEQADV 3KUA GLY A 343 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER A 344 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER A 345 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS A 346 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS A 347 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS A 348 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS A 349 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS A 350 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS A 351 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER A 352 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER A 353 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA GLY A 354 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA LEU A 355 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA VAL A 356 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA PRO A 357 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA ARG A 358 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA GLY A 359 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER A 360 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS A 361 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA MET A 362 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA MET B 342 UNP Q5E5J7 INITIATING METHIONINE SEQADV 3KUA GLY B 343 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER B 344 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER B 345 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS B 346 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS B 347 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS B 348 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS B 349 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS B 350 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS B 351 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER B 352 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER B 353 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA GLY B 354 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA LEU B 355 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA VAL B 356 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA PRO B 357 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA ARG B 358 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA GLY B 359 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA SER B 360 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA HIS B 361 UNP Q5E5J7 EXPRESSION TAG SEQADV 3KUA MET B 362 UNP Q5E5J7 EXPRESSION TAG SEQRES 1 A 153 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 153 LEU VAL PRO ARG GLY SER HIS MET THR ARG ARG THR ILE SEQRES 3 A 153 PHE GLU LEU ARG LYS ALA ARG ASP ARG ALA HIS ILE LEU SEQRES 4 A 153 GLU GLY LEU ALA LEU ALA LEU ALA ASN ILE ASP GLU ILE SEQRES 5 A 153 ILE GLU LEU ILE LYS ASN ALA PRO THR PRO ALA GLU ALA SEQRES 6 A 153 LYS GLU GLY LEU ILE SER ARG GLY TRP ASP LEU GLY ASN SEQRES 7 A 153 VAL ALA SER MET LEU GLU ARG ALA GLY THR ASP ALA ALA SEQRES 8 A 153 ARG PRO ASP TRP LEU GLU PRO GLU PHE GLY ILE ARG GLU SEQRES 9 A 153 GLY LYS TYR PHE LEU THR GLU GLN GLN ALA GLN ALA ILE SEQRES 10 A 153 LEU GLU LEU ARG LEU HIS ARG LEU THR GLY LEU GLU HIS SEQRES 11 A 153 GLU LYS ILE LEU ASP GLU TYR LYS ALA LEU LEU ASP GLU SEQRES 12 A 153 ILE ALA GLU LEU MET HIS ILE LEU ALA SER SEQRES 1 B 153 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 153 LEU VAL PRO ARG GLY SER HIS MET THR ARG ARG THR ILE SEQRES 3 B 153 PHE GLU LEU ARG LYS ALA ARG ASP ARG ALA HIS ILE LEU SEQRES 4 B 153 GLU GLY LEU ALA LEU ALA LEU ALA ASN ILE ASP GLU ILE SEQRES 5 B 153 ILE GLU LEU ILE LYS ASN ALA PRO THR PRO ALA GLU ALA SEQRES 6 B 153 LYS GLU GLY LEU ILE SER ARG GLY TRP ASP LEU GLY ASN SEQRES 7 B 153 VAL ALA SER MET LEU GLU ARG ALA GLY THR ASP ALA ALA SEQRES 8 B 153 ARG PRO ASP TRP LEU GLU PRO GLU PHE GLY ILE ARG GLU SEQRES 9 B 153 GLY LYS TYR PHE LEU THR GLU GLN GLN ALA GLN ALA ILE SEQRES 10 B 153 LEU GLU LEU ARG LEU HIS ARG LEU THR GLY LEU GLU HIS SEQRES 11 B 153 GLU LYS ILE LEU ASP GLU TYR LYS ALA LEU LEU ASP GLU SEQRES 12 B 153 ILE ALA GLU LEU MET HIS ILE LEU ALA SER SEQRES 1 C 105 MET SER GLN PHE THR LEU TYR LYS ASN LYS ASP LYS SER SEQRES 2 C 105 SER ALA LYS THR TYR PRO TYR PHE VAL ASP VAL GLN SER SEQRES 3 C 105 ASP LEU LEU ASP ASN LEU ASN THR ARG LEU VAL ILE PRO SEQRES 4 C 105 LEU THR PRO ILE GLU LEU LEU ASP LYS LYS ALA PRO SER SEQRES 5 C 105 HIS LEU CYS PRO THR ILE HIS ILE ASP GLU GLY ASP PHE SEQRES 6 C 105 ILE MET LEU THR GLN GLN MET THR SER VAL PRO VAL LYS SEQRES 7 C 105 ILE LEU SER GLU PRO VAL ASN GLU LEU SER THR PHE ARG SEQRES 8 C 105 ASN GLU ILE ILE ALA ALA ILE ASP PHE LEU ILE THR GLY SEQRES 9 C 105 ILE SEQRES 1 D 105 MET SER GLN PHE THR LEU TYR LYS ASN LYS ASP LYS SER SEQRES 2 D 105 SER ALA LYS THR TYR PRO TYR PHE VAL ASP VAL GLN SER SEQRES 3 D 105 ASP LEU LEU ASP ASN LEU ASN THR ARG LEU VAL ILE PRO SEQRES 4 D 105 LEU THR PRO ILE GLU LEU LEU ASP LYS LYS ALA PRO SER SEQRES 5 D 105 HIS LEU CYS PRO THR ILE HIS ILE ASP GLU GLY ASP PHE SEQRES 6 D 105 ILE MET LEU THR GLN GLN MET THR SER VAL PRO VAL LYS SEQRES 7 D 105 ILE LEU SER GLU PRO VAL ASN GLU LEU SER THR PHE ARG SEQRES 8 D 105 ASN GLU ILE ILE ALA ALA ILE ASP PHE LEU ILE THR GLY SEQRES 9 D 105 ILE HET GOL A 1 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *194(H2 O) HELIX 1 1 HIS A 361 ALA A 388 1 28 HELIX 2 2 ASN A 389 ASN A 399 1 11 HELIX 3 3 THR A 402 SER A 412 1 11 HELIX 4 4 LEU A 417 ASN A 419 5 3 HELIX 5 5 VAL A 420 GLU A 425 1 6 HELIX 6 6 ARG A 426 ALA A 432 1 7 HELIX 7 7 THR A 451 GLU A 460 1 10 HELIX 8 8 ARG A 462 LEU A 466 5 5 HELIX 9 9 THR A 467 LEU A 492 1 26 HELIX 10 10 MET B 362 LEU B 387 1 26 HELIX 11 11 ASN B 389 ALA B 400 1 12 HELIX 12 12 THR B 402 SER B 412 1 11 HELIX 13 13 VAL B 420 GLU B 425 1 6 HELIX 14 14 ARG B 426 ASP B 430 5 5 HELIX 15 15 THR B 451 LEU B 461 1 11 HELIX 16 16 ARG B 462 LEU B 466 5 5 HELIX 17 17 THR B 467 LEU B 492 1 26 HELIX 18 18 ASP C 11 LYS C 16 1 6 HELIX 19 19 SER C 26 ASP C 30 5 5 HELIX 20 20 GLU C 44 LEU C 46 5 3 HELIX 21 21 THR C 69 MET C 72 5 4 HELIX 22 22 LYS C 78 LEU C 80 5 3 HELIX 23 23 PHE C 90 THR C 103 1 14 HELIX 24 24 ASP D 11 LYS D 16 1 6 HELIX 25 25 SER D 26 ASP D 30 5 5 HELIX 26 26 GLU D 44 LEU D 46 5 3 HELIX 27 27 THR D 69 MET D 72 5 4 HELIX 28 28 LYS D 78 SER D 81 5 4 HELIX 29 29 PHE D 90 GLY D 104 1 15 SHEET 1 A 2 GLY A 442 ARG A 444 0 SHEET 2 A 2 LYS A 447 PHE A 449 -1 O LYS A 447 N ARG A 444 SHEET 1 B 3 TRP B 415 ASP B 416 0 SHEET 2 B 3 LYS B 447 PHE B 449 -1 O TYR B 448 N TRP B 415 SHEET 3 B 3 GLY B 442 ARG B 444 -1 N GLY B 442 O PHE B 449 SHEET 1 C 4 THR C 57 ILE C 60 0 SHEET 2 C 4 GLY C 63 MET C 67 -1 O PHE C 65 N ILE C 58 SHEET 3 C 4 THR C 34 PRO C 42 -1 N THR C 41 O ILE C 66 SHEET 4 C 4 THR C 73 PRO C 76 -1 O VAL C 75 N ARG C 35 SHEET 1 D 6 THR C 57 ILE C 60 0 SHEET 2 D 6 GLY C 63 MET C 67 -1 O PHE C 65 N ILE C 58 SHEET 3 D 6 THR C 34 PRO C 42 -1 N THR C 41 O ILE C 66 SHEET 4 D 6 TYR C 20 ASP C 23 -1 N TYR C 20 O LEU C 40 SHEET 5 D 6 THR C 5 LYS C 8 -1 N TYR C 7 O PHE C 21 SHEET 6 D 6 PRO C 83 GLU C 86 -1 O VAL C 84 N LEU C 6 SHEET 1 E 4 THR D 57 ILE D 60 0 SHEET 2 E 4 GLY D 63 MET D 67 -1 O PHE D 65 N ILE D 58 SHEET 3 E 4 THR D 34 PRO D 42 -1 N THR D 41 O ILE D 66 SHEET 4 E 4 THR D 73 PRO D 76 -1 O THR D 73 N VAL D 37 SHEET 1 F 6 THR D 57 ILE D 60 0 SHEET 2 F 6 GLY D 63 MET D 67 -1 O PHE D 65 N ILE D 58 SHEET 3 F 6 THR D 34 PRO D 42 -1 N THR D 41 O ILE D 66 SHEET 4 F 6 TYR D 20 ASP D 23 -1 N TYR D 20 O LEU D 40 SHEET 5 F 6 THR D 5 LYS D 8 -1 N TYR D 7 O PHE D 21 SHEET 6 F 6 PRO D 83 GLU D 86 -1 O VAL D 84 N LEU D 6 CISPEP 1 GLU B 445 GLY B 446 0 -7.00 SITE 1 AC1 8 ARG A 374 ALA A 377 HIS A 378 GLU A 381 SITE 2 AC1 8 THR A 429 ALA A 432 ARG A 433 PRO A 434 CRYST1 53.505 94.590 120.502 90.00 90.00 90.00 P 21 21 21 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 0.018690 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008299 0.00000