HEADER HYDROLASE 19-JAN-12 4DDW TITLE THERMOTOGA MARITIMA REVERSE GYRASE, C-CENTERED ORTHORHOMBIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: REVERSE GYRASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HELICASE, TOPOISOMERASE; COMPND 5 EC: 3.6.4.12, 5.99.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: RGY, TOPR, TM_0173; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOPOISOMERASE, DNA SUPERCOILING, ARCHAEA, HELICASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.G.RUDOLPH,D.KLOSTERMEIER REVDAT 4 13-SEP-23 4DDW 1 REMARK LINK REVDAT 3 15-NOV-17 4DDW 1 REMARK REVDAT 2 06-FEB-13 4DDW 1 JRNL REVDAT 1 26-DEC-12 4DDW 0 JRNL AUTH M.G.RUDOLPH,Y.DEL TORO DUANY,S.P.JUNGBLUT,A.GANGULY, JRNL AUTH 2 D.KLOSTERMEIER JRNL TITL CRYSTAL STRUCTURES OF THERMOTOGA MARITIMA REVERSE GYRASE: JRNL TITL 2 INFERENCES FOR THE MECHANISM OF POSITIVE DNA SUPERCOILING. JRNL REF NUCLEIC ACIDS RES. V. 41 1058 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23209025 JRNL DOI 10.1093/NAR/GKS1073 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_881) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 14446 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 716 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 48.7531 - 6.6646 1.00 2961 148 0.1643 0.2343 REMARK 3 2 6.6646 - 5.2919 1.00 2847 144 0.2460 0.3380 REMARK 3 3 5.2919 - 4.6236 0.98 2736 152 0.2082 0.3172 REMARK 3 4 4.6236 - 4.2011 0.92 2563 139 0.2403 0.3166 REMARK 3 5 4.2011 - 3.9001 0.95 2623 133 0.3070 0.3676 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 123.5 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 23.49250 REMARK 3 B22 (A**2) : 11.16540 REMARK 3 B33 (A**2) : -34.65800 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 : 0.005 9210 REMARK 3 ANGLE : 0.600 12382 REMARK 3 CHIRALITY : 0.044 1368 REMARK 3 PLANARITY : 0.002 1576 REMARK 3 DIHEDRAL : 13.570 3562 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 2:287) REMARK 3 ORIGIN FOR THE GROUP (A): -19.6544 53.2768 10.4259 REMARK 3 T TENSOR REMARK 3 T11: 1.0916 T22: 1.2076 REMARK 3 T33: 0.8833 T12: 0.1091 REMARK 3 T13: -0.0869 T23: -0.0133 REMARK 3 L TENSOR REMARK 3 L11: 3.2405 L22: 5.0877 REMARK 3 L33: 4.0759 L12: 1.8423 REMARK 3 L13: 0.5029 L23: 1.1229 REMARK 3 S TENSOR REMARK 3 S11: 0.7407 S12: -0.8344 S13: -0.2422 REMARK 3 S21: 0.6616 S22: -0.5904 S23: -0.4549 REMARK 3 S31: 0.4854 S32: -0.1665 S33: -0.1838 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 288:491) REMARK 3 ORIGIN FOR THE GROUP (A): -23.7995 78.3992 -28.1352 REMARK 3 T TENSOR REMARK 3 T11: 1.3634 T22: 1.1552 REMARK 3 T33: 1.3959 T12: -0.0127 REMARK 3 T13: -0.1112 T23: 0.0746 REMARK 3 L TENSOR REMARK 3 L11: 3.4779 L22: 2.1649 REMARK 3 L33: 5.8234 L12: 0.3617 REMARK 3 L13: -3.3217 L23: 0.1885 REMARK 3 S TENSOR REMARK 3 S11: 0.2263 S12: 0.1615 S13: 0.0950 REMARK 3 S21: 0.1225 S22: -0.4023 S23: -0.0645 REMARK 3 S31: -0.9667 S32: 0.1279 S33: 0.1937 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 492:1103) REMARK 3 ORIGIN FOR THE GROUP (A): -26.6215 36.6955 -31.7166 REMARK 3 T TENSOR REMARK 3 T11: 0.9165 T22: 1.2104 REMARK 3 T33: 1.0996 T12: 0.0475 REMARK 3 T13: -0.0447 T23: -0.0543 REMARK 3 L TENSOR REMARK 3 L11: 0.9576 L22: 1.3462 REMARK 3 L33: 3.9995 L12: 0.4263 REMARK 3 L13: -0.0183 L23: 0.5790 REMARK 3 S TENSOR REMARK 3 S11: 0.0749 S12: 0.0669 S13: -0.2104 REMARK 3 S21: 0.0634 S22: 0.0141 S23: -0.2820 REMARK 3 S31: 0.7191 S32: 0.5180 S33: -0.0538 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 4DDW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070206. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.278320 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS (VERSION DECEMBER 6 REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14481 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 5.450 REMARK 200 R MERGE (I) : 0.16220 REMARK 200 R SYM (I) : 0.16220 REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.54 REMARK 200 R MERGE FOR SHELL (I) : 0.82730 REMARK 200 R SYM FOR SHELL (I) : 0.82730 REMARK 200 FOR SHELL : 1.230 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 4DDT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MG(OAC)2, 20% PEG3350, 0.15M REMARK 280 SODIUM CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 52.06750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.06750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 87.16250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 87.82300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 87.16250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 87.82300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.06750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 87.16250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 87.82300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.06750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 87.16250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 87.82300 REMARK 290 SMTRY3 8 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 1104 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 ASN A 4 85.32 -55.69 REMARK 500 PRO A 28 -174.44 -67.03 REMARK 500 LYS A 77 -168.50 -104.82 REMARK 500 LEU A 144 -15.02 -145.35 REMARK 500 HIS A 176 -40.21 -132.52 REMARK 500 ARG A 296 44.78 -88.59 REMARK 500 ARG A 309 -107.23 59.49 REMARK 500 GLN A 317 -75.67 -55.40 REMARK 500 SER A 341 -62.08 -123.82 REMARK 500 GLU A 342 66.14 -109.59 REMARK 500 LYS A 367 -24.43 -142.81 REMARK 500 ASP A 373 83.48 59.10 REMARK 500 GLU A 394 -113.71 -131.81 REMARK 500 ASP A 396 -158.07 -109.19 REMARK 500 LYS A 397 -14.77 67.15 REMARK 500 LEU A 412 -27.11 -141.23 REMARK 500 ALA A 415 77.39 -68.44 REMARK 500 ASP A 461 90.28 -69.63 REMARK 500 ILE A 505 -71.29 -86.71 REMARK 500 GLU A 515 42.59 -88.23 REMARK 500 ALA A 563 -65.90 -102.54 REMARK 500 ARG A 569 -111.56 52.07 REMARK 500 THR A 578 -169.34 -115.42 REMARK 500 ARG A 589 60.32 60.79 REMARK 500 ILE A 601 86.20 -69.32 REMARK 500 HIS A 602 -40.61 64.28 REMARK 500 SER A 687 -76.32 -77.86 REMARK 500 ARG A 689 32.90 -90.66 REMARK 500 SER A 710 56.53 -111.66 REMARK 500 SER A 747 -78.58 -67.71 REMARK 500 LEU A 749 -70.42 -126.75 REMARK 500 ALA A 794 40.29 -150.17 REMARK 500 LYS A 876 66.56 -118.54 REMARK 500 TRP A 885 -52.00 63.08 REMARK 500 PRO A 899 69.34 -64.00 REMARK 500 ILE A 914 -73.09 -124.58 REMARK 500 VAL A 942 -161.62 -126.19 REMARK 500 HIS A 983 44.27 -98.31 REMARK 500 ARG A 984 -161.61 -124.70 REMARK 500 LYS A 995 65.25 -152.01 REMARK 500 PRO A1019 -31.68 -35.65 REMARK 500 TYR A1022 -70.69 -47.15 REMARK 500 ASP A1038 -149.69 -133.73 REMARK 500 ARG A1059 -70.06 -102.65 REMARK 500 GLU A1102 58.13 -92.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 914 ALA A 915 -144.79 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 ZN A1202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 11 SG REMARK 620 2 CYS A 14 SG 104.4 REMARK 620 3 CYS A 29 SG 109.7 110.8 REMARK 620 4 CYS A 32 SG 117.7 110.7 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 107 OG1 REMARK 620 2 ASP A 203 OD1 79.7 REMARK 620 3 POP A1203 O1 92.4 158.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 621 SG REMARK 620 2 CYS A 624 SG 112.5 REMARK 620 3 CYS A 635 SG 113.8 105.9 REMARK 620 4 CYS A 638 SG 103.2 109.0 112.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DDT RELATED DB: PDB REMARK 900 RELATED ID: 4DDU RELATED DB: PDB REMARK 900 RELATED ID: 4DDV RELATED DB: PDB REMARK 900 RELATED ID: 4DDX RELATED DB: PDB DBREF 4DDW A 1 1104 UNP O51934 RGYR_THEMA 1 1104 SEQRES 1 A 1104 MET ALA VAL ASN SER LYS TYR HIS HIS SER CYS ILE ASN SEQRES 2 A 1104 CYS GLY GLY LEU ASN THR ASP GLU ARG ASN GLU ARG GLY SEQRES 3 A 1104 LEU PRO CYS GLU VAL CYS LEU PRO GLU ASP SER PRO SER SEQRES 4 A 1104 ASP ILE TYR ARG ALA LEU LEU GLU ARG LYS THR LEU LYS SEQRES 5 A 1104 GLU TYR ARG PHE TYR HIS GLU PHE TRP ASN GLU TYR GLU SEQRES 6 A 1104 ASP PHE ARG SER PHE PHE LYS LYS LYS PHE GLY LYS ASP SEQRES 7 A 1104 LEU THR GLY TYR GLN ARG LEU TRP ALA LYS ARG ILE VAL SEQRES 8 A 1104 GLN GLY LYS SER PHE THR MET VAL ALA PRO THR GLY VAL SEQRES 9 A 1104 GLY LYS THR THR PHE GLY MET MET THR ALA LEU TRP LEU SEQRES 10 A 1104 ALA ARG LYS GLY LYS LYS SER ALA LEU VAL PHE PRO THR SEQRES 11 A 1104 VAL THR LEU VAL LYS GLN THR LEU GLU ARG LEU GLN LYS SEQRES 12 A 1104 LEU ALA ASP GLU LYS VAL LYS ILE PHE GLY PHE TYR SER SEQRES 13 A 1104 SER MET LYS LYS GLU GLU LYS GLU LYS PHE GLU LYS SER SEQRES 14 A 1104 PHE GLU GLU ASP ASP TYR HIS ILE LEU VAL PHE SER THR SEQRES 15 A 1104 GLN PHE VAL SER LYS ASN ARG GLU LYS LEU SER GLN LYS SEQRES 16 A 1104 ARG PHE ASP PHE VAL PHE VAL ASP ASP VAL ASP ALA VAL SEQRES 17 A 1104 LEU LYS ALA SER ARG ASN ILE ASP THR LEU LEU MET MET SEQRES 18 A 1104 VAL GLY ILE PRO GLU GLU ILE ILE ARG LYS ALA PHE SER SEQRES 19 A 1104 THR ILE LYS GLN GLY LYS ILE TYR GLU ARG PRO LYS ASN SEQRES 20 A 1104 LEU LYS PRO GLY ILE LEU VAL VAL SER SER ALA THR ALA SEQRES 21 A 1104 LYS PRO ARG GLY ILE ARG PRO LEU LEU PHE ARG ASP LEU SEQRES 22 A 1104 LEU ASN PHE THR VAL GLY ARG LEU VAL SER VAL ALA ARG SEQRES 23 A 1104 ASN ILE THR HIS VAL ARG ILE SER SER ARG SER LYS GLU SEQRES 24 A 1104 LYS LEU VAL GLU LEU LEU GLU ILE PHE ARG ASP GLY ILE SEQRES 25 A 1104 LEU ILE PHE ALA GLN THR GLU GLU GLU GLY LYS GLU LEU SEQRES 26 A 1104 TYR GLU TYR LEU LYS ARG PHE LYS PHE ASN VAL GLY GLU SEQRES 27 A 1104 THR TRP SER GLU PHE GLU LYS ASN PHE GLU ASP PHE LYS SEQRES 28 A 1104 VAL GLY LYS ILE ASN ILE LEU ILE GLY VAL GLN ALA TYR SEQRES 29 A 1104 TYR GLY LYS LEU THR ARG GLY VAL ASP LEU PRO GLU ARG SEQRES 30 A 1104 ILE LYS TYR VAL ILE PHE TRP GLY THR PRO SER MET ARG SEQRES 31 A 1104 PHE SER LEU GLU LEU ASP LYS ALA PRO ARG PHE VAL LEU SEQRES 32 A 1104 ALA ARG VAL LEU LYS GLU MET GLY LEU ILE LYS ALA GLN SEQRES 33 A 1104 GLU ASN PRO ASP VAL GLU GLU LEU ARG LYS ILE ALA LYS SEQRES 34 A 1104 GLU HIS LEU THR GLN LYS GLU PHE VAL GLU LYS VAL LYS SEQRES 35 A 1104 GLU MET PHE ARG GLY VAL VAL VAL LYS ASP GLU ASP LEU SEQRES 36 A 1104 GLU LEU ILE ILE PRO ASP VAL TYR THR TYR ILE GLN ALA SEQRES 37 A 1104 SER GLY ARG SER SER ARG ILE LEU ASN GLY VAL LEU VAL SEQRES 38 A 1104 LYS GLY VAL SER VAL ILE PHE GLU GLU ASP GLU GLU ILE SEQRES 39 A 1104 PHE GLU SER LEU LYS THR ARG LEU LEU LEU ILE ALA GLU SEQRES 40 A 1104 GLU GLU ILE ILE GLU GLU ALA GLU ALA ASN TRP LYS GLU SEQRES 41 A 1104 LEU VAL HIS GLU VAL GLU GLU SER ARG ARG ARG SER GLU SEQRES 42 A 1104 ARG GLU LEU THR ASP THR SER ARG SER LEU LEU ILE ILE SEQRES 43 A 1104 VAL GLU SER PRO THR LYS ALA GLU THR LEU SER ARG PHE SEQRES 44 A 1104 LEU GLY ARG ALA SER SER ARG LYS GLU ARG ASN ILE ILE SEQRES 45 A 1104 VAL HIS GLU ALA VAL THR GLY GLU GLY VAL ILE LEU PHE SEQRES 46 A 1104 THR ALA THR ARG GLY HIS VAL TYR ASP LEU VAL THR LYS SEQRES 47 A 1104 GLY GLY ILE HIS GLY VAL GLU GLU GLU ASN GLY LYS PHE SEQRES 48 A 1104 VAL PRO VAL TYR ASN SER LEU LYS ARG CYS ARG ASP CYS SEQRES 49 A 1104 GLY TYR GLN PHE THR GLU ASP ARG ASP GLU CYS PRO VAL SEQRES 50 A 1104 CYS SER SER LYS ASN ILE ASP ASP LYS THR GLU THR LEU SEQRES 51 A 1104 ARG ALA LEU ARG GLU ILE SER LEU GLU ALA ASP GLU ILE SEQRES 52 A 1104 LEU VAL ALA THR ASP PRO ASP VAL GLU GLY GLU LYS ILE SEQRES 53 A 1104 SER TRP ASP VAL THR GLN TYR LEU LEU PRO SER THR ARG SEQRES 54 A 1104 SER LEU ARG ARG ILE GLU MET HIS GLU ILE THR ARG TYR SEQRES 55 A 1104 GLY PHE LYS LYS ALA ARG GLU SER VAL ARG PHE VAL ASP SEQRES 56 A 1104 PHE ASN LEU VAL LYS ALA GLN ILE VAL ARG ARG VAL GLN SEQRES 57 A 1104 ASP ARG TRP ILE GLY PHE GLU LEU SER GLY LYS LEU GLN SEQRES 58 A 1104 LYS ARG PHE GLY ARG SER ASN LEU SER ALA GLY ARG VAL SEQRES 59 A 1104 GLN SER THR VAL LEU GLY TRP ILE VAL GLU ARG GLU GLU SEQRES 60 A 1104 GLU TYR LYS LYS SER GLU LYS ASP PHE THR LEU LEU VAL SEQRES 61 A 1104 LEU GLU ASN GLY VAL ASN LEU GLU VAL GLU GLY LYS ILE SEQRES 62 A 1104 ALA ASP ASP VAL VAL THR VAL VAL GLU LEU GLN GLU ALA SEQRES 63 A 1104 GLU GLU GLU LYS ASN PRO LEU PRO PRO TYR THR THR SER SEQRES 64 A 1104 SER ALA LEU SER GLU ILE SER GLN LYS LEU ARG LEU GLY SEQRES 65 A 1104 VAL GLN GLU VAL MET ASP ILE LEU GLN ASP LEU PHE GLU SEQRES 66 A 1104 LYS GLY PHE ILE THR TYR HIS ARG THR ASP SER THR ARG SEQRES 67 A 1104 ILE SER LEU GLU GLY GLN ASN VAL ALA ARG THR TYR LEU SEQRES 68 A 1104 ARG LYS ILE GLY LYS GLU ASP ILE PHE MET GLY ARG SER SEQRES 69 A 1104 TRP SER THR GLU GLY ALA HIS GLU ALA ILE ARG PRO VAL SEQRES 70 A 1104 LYS PRO ILE ASP ALA ARG GLU LEU GLU GLU MET ILE GLU SEQRES 71 A 1104 GLU GLY LEU ILE ALA ASP LEU THR LYS LYS HIS LEU ARG SEQRES 72 A 1104 VAL TYR GLU LEU ILE PHE ASN ARG PHE LEU ALA SER GLN SEQRES 73 A 1104 SER ALA ALA VAL LYS VAL LYS LYS GLN ILE VAL THR VAL SEQRES 74 A 1104 ASP VAL ASP GLY LYS ARG MET GLY ILE GLU GLN ILE VAL SEQRES 75 A 1104 GLU ILE LEU ARG ASP GLY TRP ASN LEU PHE VAL PRO LEU SEQRES 76 A 1104 THR VAL SER PRO ARG PHE GLU HIS ARG THR TYR LYS ILE SEQRES 77 A 1104 LYS GLU LYS LYS PHE TYR LYS LYS HIS THR VAL PRO LEU SEQRES 78 A 1104 PHE THR GLN ALA SER ILE VAL GLU GLU MET LYS LYS ARG SEQRES 79 A 1104 GLY ILE GLY ARG PRO SER THR TYR ALA LYS ILE VAL GLU SEQRES 80 A 1104 VAL LEU PHE ARG ARG GLY TYR VAL TYR GLU ASP LYS TYR SEQRES 81 A 1104 LYS ARG VAL ARG PRO THR ARG PHE GLY VAL MET VAL TYR SEQRES 82 A 1104 SER TYR LEU LYS GLU ARG TYR GLU LYS TYR VAL THR GLU SEQRES 83 A 1104 GLU THR THR ARG ARG LEU GLU GLU ILE MET ASP LYS VAL SEQRES 84 A 1104 GLU ARG GLY GLU GLU ASP TYR GLN ALA THR LEU ARG LEU SEQRES 85 A 1104 LEU TYR GLU GLU ILE LYS SER LEU MET GLU GLU GLY HET ZN A1201 1 HET ZN A1202 1 HET POP A1203 9 HET MG A1204 1 HETNAM ZN ZINC ION HETNAM POP PYROPHOSPHATE 2- HETNAM MG MAGNESIUM ION FORMUL 2 ZN 2(ZN 2+) FORMUL 4 POP H2 O7 P2 2- FORMUL 5 MG MG 2+ HELIX 1 1 ASP A 20 GLY A 26 1 7 HELIX 2 2 ASP A 40 GLU A 47 1 8 HELIX 3 3 GLU A 53 PHE A 75 1 23 HELIX 4 4 THR A 80 VAL A 91 1 12 HELIX 5 5 GLY A 105 GLY A 121 1 17 HELIX 6 6 THR A 130 LYS A 143 1 14 HELIX 7 7 GLU A 161 GLU A 172 1 12 HELIX 8 8 THR A 182 ASN A 188 1 7 HELIX 9 9 ASN A 188 GLN A 194 1 7 HELIX 10 10 ASP A 204 LEU A 209 1 6 HELIX 11 11 SER A 212 GLY A 223 1 12 HELIX 12 12 PRO A 225 GLY A 239 1 15 HELIX 13 13 PRO A 267 LEU A 274 1 8 HELIX 14 14 SER A 297 ARG A 309 1 13 HELIX 15 15 THR A 318 PHE A 332 1 15 HELIX 16 16 GLU A 344 GLY A 353 1 10 HELIX 17 17 PRO A 399 GLY A 411 1 13 HELIX 18 18 ASP A 420 LEU A 432 1 13 HELIX 19 19 THR A 433 PHE A 445 1 13 HELIX 20 20 ASP A 461 GLY A 470 1 10 HELIX 21 21 ARG A 471 SER A 473 5 3 HELIX 22 22 ASP A 491 ILE A 505 1 15 HELIX 23 23 ASN A 517 ARG A 534 1 18 HELIX 24 24 SER A 549 GLY A 561 1 13 HELIX 25 25 LYS A 646 SER A 657 1 12 HELIX 26 26 ASP A 670 LEU A 685 1 16 HELIX 27 27 THR A 700 SER A 710 1 11 HELIX 28 28 ASP A 715 LYS A 742 1 28 HELIX 29 29 GLY A 752 TYR A 769 1 18 HELIX 30 30 THR A 817 LEU A 829 1 13 HELIX 31 31 GLY A 832 LYS A 846 1 15 HELIX 32 32 SER A 860 GLY A 875 1 16 HELIX 33 33 ASP A 901 GLY A 912 1 12 HELIX 34 34 THR A 918 SER A 935 1 18 HELIX 35 35 GLY A 968 PHE A 972 5 5 HELIX 36 36 THR A 1003 ARG A 1014 1 12 HELIX 37 37 THR A 1021 GLY A 1033 1 13 HELIX 38 38 THR A 1046 TYR A 1060 1 15 HELIX 39 39 THR A 1065 GLU A 1080 1 16 HELIX 40 40 ASP A 1085 GLU A 1102 1 18 SHEET 1 A 4 ASN A 18 THR A 19 0 SHEET 2 A 4 LYS A 6 TYR A 7 -1 N TYR A 7 O ASN A 18 SHEET 3 A 4 LYS A 610 SER A 617 1 O TYR A 615 N LYS A 6 SHEET 4 A 4 TYR A 593 LEU A 595 -1 N ASP A 594 O ASN A 616 SHEET 1 B 4 ASN A 18 THR A 19 0 SHEET 2 B 4 LYS A 6 TYR A 7 -1 N TYR A 7 O ASN A 18 SHEET 3 B 4 LYS A 610 SER A 617 1 O TYR A 615 N LYS A 6 SHEET 4 B 4 VAL A 604 GLU A 607 -1 N GLU A 605 O VAL A 612 SHEET 1 C 6 PHE A 96 MET A 98 0 SHEET 2 C 6 LEU A 253 SER A 256 1 O VAL A 255 N MET A 98 SHEET 3 C 6 PHE A 199 VAL A 202 1 N VAL A 200 O VAL A 254 SHEET 4 C 6 SER A 124 PHE A 128 1 N VAL A 127 O PHE A 201 SHEET 5 C 6 ILE A 177 SER A 181 1 O LEU A 178 N LEU A 126 SHEET 6 C 6 ILE A 151 PHE A 154 1 N PHE A 152 O VAL A 179 SHEET 1 D 6 ILE A 357 VAL A 361 0 SHEET 2 D 6 ILE A 312 ALA A 316 1 N ILE A 314 O GLY A 360 SHEET 3 D 6 TYR A 380 TRP A 384 1 O ILE A 382 N LEU A 313 SHEET 4 D 6 GLY A 483 PHE A 488 1 O VAL A 486 N PHE A 383 SHEET 5 D 6 ILE A 288 ILE A 293 1 N ILE A 293 O ILE A 487 SHEET 6 D 6 ILE A 510 GLU A 512 1 O ILE A 511 N HIS A 290 SHEET 1 E 3 SER A 388 SER A 392 0 SHEET 2 E 3 GLU A 456 PRO A 460 -1 O ILE A 459 N MET A 389 SHEET 3 E 3 VAL A 449 LYS A 451 -1 N VAL A 449 O ILE A 458 SHEET 1 F 2 ILE A 475 LEU A 476 0 SHEET 2 F 2 VAL A 479 LEU A 480 -1 O VAL A 479 N LEU A 476 SHEET 1 G 6 ARG A 562 GLU A 568 0 SHEET 2 G 6 ILE A 571 VAL A 577 -1 O GLU A 575 N SER A 564 SHEET 3 G 6 GLY A 581 ALA A 587 -1 O PHE A 585 N HIS A 574 SHEET 4 G 6 ARG A 541 VAL A 547 1 N LEU A 543 O LEU A 584 SHEET 5 G 6 GLU A 662 VAL A 665 1 O LEU A 664 N LEU A 544 SHEET 6 G 6 LEU A 691 ARG A 693 1 O ARG A 692 N ILE A 663 SHEET 1 H 3 GLN A 627 PHE A 628 0 SHEET 2 H 3 LYS A 619 CYS A 621 -1 N LYS A 619 O PHE A 628 SHEET 3 H 3 ILE A 643 ASP A 645 -1 O ASP A 644 N ARG A 620 SHEET 1 I 6 ASN A 786 GLU A 790 0 SHEET 2 I 6 PHE A 776 LEU A 781 -1 N THR A 777 O VAL A 789 SHEET 3 I 6 THR A 985 TYR A 994 -1 O TYR A 994 N PHE A 776 SHEET 4 I 6 VAL A 797 ALA A 806 -1 N VAL A 798 O TYR A 986 SHEET 5 I 6 VAL A 940 VAL A 951 -1 O ASP A 950 N THR A 799 SHEET 6 I 6 GLU A 809 LYS A 810 -1 N LYS A 810 O VAL A 940 SHEET 1 J 6 ASN A 786 GLU A 790 0 SHEET 2 J 6 PHE A 776 LEU A 781 -1 N THR A 777 O VAL A 789 SHEET 3 J 6 THR A 985 TYR A 994 -1 O TYR A 994 N PHE A 776 SHEET 4 J 6 VAL A 797 ALA A 806 -1 N VAL A 798 O TYR A 986 SHEET 5 J 6 VAL A 940 VAL A 951 -1 O ASP A 950 N THR A 799 SHEET 6 J 6 LYS A 954 ARG A 966 -1 O ILE A 958 N VAL A 947 SHEET 1 K 2 VAL A1035 TYR A1036 0 SHEET 2 K 2 ARG A1044 PRO A1045 -1 O ARG A1044 N TYR A1036 LINK SG CYS A 11 ZN ZN A1202 1555 1555 2.36 LINK SG CYS A 14 ZN ZN A1202 1555 1555 2.28 LINK SG CYS A 29 ZN ZN A1202 1555 1555 2.28 LINK SG CYS A 32 ZN ZN A1202 1555 1555 2.38 LINK OG1 THR A 107 MG MG A1204 1555 1555 1.96 LINK OD1 ASP A 203 MG MG A1204 1555 1555 2.08 LINK SG CYS A 621 ZN ZN A1201 1555 1555 2.30 LINK SG CYS A 624 ZN ZN A1201 1555 1555 2.26 LINK SG CYS A 635 ZN ZN A1201 1555 1555 2.34 LINK SG CYS A 638 ZN ZN A1201 1555 1555 2.23 LINK O1 POP A1203 MG MG A1204 1555 1555 2.49 SITE 1 AC1 4 CYS A 621 CYS A 624 CYS A 635 CYS A 638 SITE 1 AC2 4 CYS A 11 CYS A 14 CYS A 29 CYS A 32 SITE 1 AC3 7 GLY A 103 VAL A 104 GLY A 105 LYS A 106 SITE 2 AC3 7 THR A 107 THR A 108 MG A1204 SITE 1 AC4 3 THR A 107 ASP A 203 POP A1203 CRYST1 174.325 175.646 104.135 90.00 90.00 90.00 C 2 2 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 0.005736 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005693 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009603 0.00000