HEADER TRANSFERASE 08-JAN-15 4XJ3 TITLE CRYSTAL STRUCTURE OF VIBRIO CHOLERAE DNCV GTP BOUND FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC AMP-GMP SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-215, 242-412; COMPND 5 SYNONYM: C-AMP-GMP SYNTHASE,DINUCLEOTIDE CYCLASE DNCV; COMPND 6 EC: 2.7.7.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961; SOURCE 3 ORGANISM_TAXID: 243277; SOURCE 4 STRAIN: N16961; SOURCE 5 GENE: DNCV, VC_0179; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLIC GMP-AMP SYNTHASE, BACTERIAL VIRULENCE, NUCLEOTIDYLTRANSFERASE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KATO,R.ISHII,R.ISHITANI,O.NUREKI REVDAT 4 08-NOV-23 4XJ3 1 LINK REVDAT 3 05-FEB-20 4XJ3 1 SOURCE JRNL REMARK REVDAT 2 20-MAY-15 4XJ3 1 JRNL REVDAT 1 29-APR-15 4XJ3 0 JRNL AUTH K.KATO,R.ISHII,S.HIRANO,R.ISHITANI,O.NUREKI JRNL TITL STRUCTURAL BASIS FOR THE CATALYTIC MECHANISM OF DNCV, JRNL TITL 2 BACTERIAL HOMOLOG OF CYCLIC GMP-AMP SYNTHASE JRNL REF STRUCTURE V. 23 843 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25865248 JRNL DOI 10.1016/J.STR.2015.01.023 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 49987 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2513 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 45.9711 - 4.3230 0.99 2793 147 0.1580 0.1837 REMARK 3 2 4.3230 - 3.4316 1.00 2753 142 0.1563 0.2001 REMARK 3 3 3.4316 - 2.9980 0.99 2723 143 0.1776 0.1983 REMARK 3 4 2.9980 - 2.7239 0.99 2694 142 0.1896 0.1890 REMARK 3 5 2.7239 - 2.5287 0.99 2695 140 0.1725 0.2161 REMARK 3 6 2.5287 - 2.3796 0.99 2674 140 0.1721 0.1963 REMARK 3 7 2.3796 - 2.2604 0.99 2683 146 0.1696 0.2174 REMARK 3 8 2.2604 - 2.1620 0.99 2683 141 0.1626 0.1954 REMARK 3 9 2.1620 - 2.0788 0.99 2650 132 0.1688 0.2040 REMARK 3 10 2.0788 - 2.0071 0.98 2662 157 0.1775 0.2077 REMARK 3 11 2.0071 - 1.9443 0.98 2685 133 0.1874 0.2102 REMARK 3 12 1.9443 - 1.8887 0.98 2621 149 0.1915 0.2424 REMARK 3 13 1.8887 - 1.8390 0.98 2635 128 0.1869 0.2716 REMARK 3 14 1.8390 - 1.7941 0.98 2672 140 0.2015 0.2367 REMARK 3 15 1.7941 - 1.7533 0.98 2620 148 0.2086 0.2247 REMARK 3 16 1.7533 - 1.7160 0.98 2636 128 0.2179 0.2413 REMARK 3 17 1.7160 - 1.6817 0.93 2509 138 0.2551 0.2734 REMARK 3 18 1.6817 - 1.6500 0.78 2086 119 0.2722 0.3197 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.570 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) : 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 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 : 0.007 3095 REMARK 3 ANGLE : 1.102 4181 REMARK 3 CHIRALITY : 0.042 456 REMARK 3 PLANARITY : 0.004 527 REMARK 3 DIHEDRAL : 16.504 1167 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 93 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.2520 28.0627 71.9942 REMARK 3 T TENSOR REMARK 3 T11: 0.3317 T22: 0.2874 REMARK 3 T33: 0.1866 T12: -0.0923 REMARK 3 T13: -0.0201 T23: 0.0418 REMARK 3 L TENSOR REMARK 3 L11: 0.9513 L22: 1.7266 REMARK 3 L33: 4.4026 L12: 1.0428 REMARK 3 L13: -2.0042 L23: -2.9962 REMARK 3 S TENSOR REMARK 3 S11: 0.1903 S12: -0.3048 S13: -0.1130 REMARK 3 S21: 0.4253 S22: -0.2420 S23: -0.0424 REMARK 3 S31: -0.5991 S32: 0.4203 S33: 0.0238 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.8801 23.1270 68.3881 REMARK 3 T TENSOR REMARK 3 T11: 0.2846 T22: 0.2393 REMARK 3 T33: 0.2278 T12: -0.0552 REMARK 3 T13: -0.0047 T23: 0.0586 REMARK 3 L TENSOR REMARK 3 L11: 1.0604 L22: 0.7471 REMARK 3 L33: 3.0351 L12: 0.0659 REMARK 3 L13: -0.7703 L23: -1.4264 REMARK 3 S TENSOR REMARK 3 S11: 0.0568 S12: -0.2724 S13: -0.2563 REMARK 3 S21: 0.2042 S22: -0.1186 S23: 0.0824 REMARK 3 S31: -0.0254 S32: 0.2177 S33: 0.0435 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 412 ) REMARK 3 ORIGIN FOR THE GROUP (A): 40.2605 33.2539 40.8339 REMARK 3 T TENSOR REMARK 3 T11: 0.0811 T22: 0.0760 REMARK 3 T33: 0.0976 T12: 0.0086 REMARK 3 T13: -0.0186 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 1.5674 L22: 1.3569 REMARK 3 L33: 1.0454 L12: 0.5315 REMARK 3 L13: -0.3242 L23: -0.1942 REMARK 3 S TENSOR REMARK 3 S11: 0.0552 S12: 0.0076 S13: -0.0720 REMARK 3 S21: 0.0367 S22: -0.0719 S23: 0.0170 REMARK 3 S31: 0.0335 S32: 0.0093 S33: 0.0147 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 4XJ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205769. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 - 6.7 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49988 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4XJ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, SODIUM FLUORIDE, BIS-TRIS REMARK 280 PROPANE, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 59.39000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.92500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.39000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.92500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1112 LIES ON A SPECIAL POSITION. 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 GLU A 144 REMARK 465 SER A 145 REMARK 465 GLU A 146 REMARK 465 PRO A 147 REMARK 465 GLU A 203 REMARK 465 PHE A 204 REMARK 465 GLN A 205 REMARK 465 LYS A 206 REMARK 465 LYS A 207 REMARK 465 GLN A 208 REMARK 465 ILE A 209 REMARK 465 ALA A 210 REMARK 465 LEU A 211 REMARK 465 GLU A 212 REMARK 465 ALA A 213 REMARK 465 ASN A 214 REMARK 465 ARG A 215 REMARK 465 GLY A 239 REMARK 465 SER A 240 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 2 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 ARG A 44 CZ NH1 NH2 REMARK 470 ARG A 108 CZ NH1 NH2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 ASP A 202 CG OD1 OD2 REMARK 470 GLU A 243 CG CD OE1 OE2 REMARK 470 ASP A 253 CG OD1 OD2 REMARK 470 LYS A 350 CG CD CE NZ 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 O2A GTP A 1013 O HOH A 1324 2.02 REMARK 500 O HOH A 1219 O HOH A 1339 2.04 REMARK 500 O HOH A 1156 O HOH A 1174 2.10 REMARK 500 OD2 ASP A 384 O HOH A 1101 2.14 REMARK 500 O HOH A 1138 O HOH A 1159 2.15 REMARK 500 O HOH A 1239 O HOH A 1277 2.17 REMARK 500 O HOH A 1281 O HOH A 1291 2.19 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 ASP A 16 20.09 -142.50 REMARK 500 PHE A 124 -65.18 -107.92 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 A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD2 REMARK 620 2 ASP A 133 OD2 77.7 REMARK 620 3 GTP A1012 O2G 102.3 178.9 REMARK 620 4 GTP A1012 O2B 168.9 98.8 81.4 REMARK 620 5 GTP A1012 O2A 89.5 95.4 85.7 80.3 REMARK 620 6 HOH A1320 O 101.7 87.5 91.4 88.6 168.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD2 REMARK 620 2 GTP A1012 O2A 90.6 REMARK 620 3 GTP A1013 O3' 92.0 95.6 REMARK 620 4 HOH A1322 O 88.2 89.8 174.6 REMARK 620 5 HOH A1323 O 79.1 169.0 88.6 86.1 REMARK 620 6 HOH A1327 O 171.7 84.9 95.4 84.8 104.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 1013 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XJ1 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ4 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ5 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ6 RELATED DB: PDB DBREF 4XJ3 A 1 215 UNP Q9KVG7 DNCV_VIBCH 1 215 DBREF 4XJ3 A 242 412 UNP Q9KVG7 DNCV_VIBCH 242 412 SEQADV 4XJ3 GLY A 239 UNP Q9KVG7 LINKER SEQADV 4XJ3 SER A 240 UNP Q9KVG7 LINKER SEQADV 4XJ3 GLY A 241 UNP Q9KVG7 LINKER SEQRES 1 A 389 MET ARG MET THR TRP ASN PHE HIS GLN TYR TYR THR ASN SEQRES 2 A 389 ARG ASN ASP GLY LEU MET GLY LYS LEU VAL LEU THR ASP SEQRES 3 A 389 GLU GLU LYS ASN ASN LEU LYS ALA LEU ARG LYS ILE ILE SEQRES 4 A 389 ARG LEU ARG THR ARG ASP VAL PHE GLU GLU ALA LYS GLY SEQRES 5 A 389 ILE ALA LYS ALA VAL LYS LYS SER ALA LEU THR PHE GLU SEQRES 6 A 389 ILE ILE GLN GLU LYS VAL SER THR THR GLN ILE LYS HIS SEQRES 7 A 389 LEU SER ASP SER GLU GLN ARG GLU VAL ALA LYS LEU ILE SEQRES 8 A 389 TYR GLU MET ASP ASP ASP ALA ARG ASP GLU PHE LEU GLY SEQRES 9 A 389 LEU THR PRO ARG PHE TRP THR GLN GLY SER PHE GLN TYR SEQRES 10 A 389 ASP THR LEU ASN ARG PRO PHE GLN PRO GLY GLN GLU MET SEQRES 11 A 389 ASP ILE ASP ASP GLY THR TYR MET PRO MET PRO ILE PHE SEQRES 12 A 389 GLU SER GLU PRO LYS ILE GLY HIS SER LEU LEU ILE LEU SEQRES 13 A 389 LEU VAL ASP ALA SER LEU LYS SER LEU VAL ALA GLU ASN SEQRES 14 A 389 HIS GLY TRP LYS PHE GLU ALA LYS GLN THR CYS GLY ARG SEQRES 15 A 389 ILE LYS ILE GLU ALA GLU LYS THR HIS ILE ASP VAL PRO SEQRES 16 A 389 MET TYR ALA ILE PRO LYS ASP GLU PHE GLN LYS LYS GLN SEQRES 17 A 389 ILE ALA LEU GLU ALA ASN ARG GLY SER GLY SER GLU ASN SEQRES 18 A 389 VAL ASN LEU ALA LEU ARG GLU GLY ASP ARG LYS TRP ILE SEQRES 19 A 389 ASN SER ASP PRO LYS ILE VAL GLU ASP TRP PHE ASN ASP SEQRES 20 A 389 SER CYS ILE ARG ILE GLY LYS HIS LEU ARG LYS VAL CYS SEQRES 21 A 389 ARG PHE MET LYS ALA TRP ARG ASP ALA GLN TRP ASP VAL SEQRES 22 A 389 GLY GLY PRO SER SER ILE SER LEU MET ALA ALA THR VAL SEQRES 23 A 389 ASN ILE LEU ASP SER VAL ALA HIS ASP ALA SER ASP LEU SEQRES 24 A 389 GLY GLU THR MET LYS ILE ILE ALA LYS HIS LEU PRO SER SEQRES 25 A 389 GLU PHE ALA ARG GLY VAL GLU SER PRO ASP SER THR ASP SEQRES 26 A 389 GLU LYS PRO LEU PHE PRO PRO SER TYR LYS HIS GLY PRO SEQRES 27 A 389 ARG GLU MET ASP ILE MET SER LYS LEU GLU ARG LEU PRO SEQRES 28 A 389 GLU ILE LEU SER SER ALA GLU SER ALA ASP SER LYS SER SEQRES 29 A 389 GLU ALA LEU LYS LYS ILE ASN MET ALA PHE GLY ASN ARG SEQRES 30 A 389 VAL THR ASN SER GLU LEU ILE VAL LEU ALA LYS ALA HET MG A1001 1 HET MG A1002 1 HET EDO A1003 4 HET EDO A1004 4 HET EDO A1005 4 HET EDO A1006 4 HET EDO A1007 4 HET EDO A1008 4 HET EDO A1009 4 HET EDO A1010 4 HET EDO A1011 4 HET GTP A1012 32 HET GTP A1013 32 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG 2(MG 2+) FORMUL 4 EDO 9(C2 H6 O2) FORMUL 13 GTP 2(C10 H16 N5 O14 P3) FORMUL 15 HOH *263(H2 O) HELIX 1 AA1 PHE A 7 ASN A 13 1 7 HELIX 2 AA2 GLY A 17 VAL A 23 1 7 HELIX 3 AA3 THR A 25 SER A 60 1 36 HELIX 4 AA4 THR A 63 THR A 73 1 11 HELIX 5 AA5 THR A 74 LEU A 79 5 6 HELIX 6 AA6 SER A 80 MET A 94 1 15 HELIX 7 AA7 ASP A 95 GLY A 104 1 10 HELIX 8 AA8 GLY A 150 ASN A 169 1 20 HELIX 9 AA9 GLY A 241 ASN A 244 5 4 HELIX 10 AB1 ASP A 260 GLY A 276 1 17 HELIX 11 AB2 LYS A 277 TRP A 294 1 18 HELIX 12 AB3 SER A 300 VAL A 315 1 16 HELIX 13 AB4 ASP A 321 ARG A 339 1 19 HELIX 14 AB5 PRO A 355 HIS A 359 5 5 HELIX 15 AB6 GLY A 360 SER A 382 1 23 HELIX 16 AB7 SER A 385 GLY A 398 1 14 HELIX 17 AB8 ASN A 403 ILE A 407 5 5 SHEET 1 AA1 2 MET A 3 ASN A 6 0 SHEET 2 AA1 2 VAL A 408 LYS A 411 -1 O VAL A 408 N ASN A 6 SHEET 1 AA2 5 ARG A 108 GLN A 112 0 SHEET 2 AA2 5 MET A 130 MET A 140 -1 O TYR A 137 N ARG A 108 SHEET 3 AA2 5 THR A 190 VAL A 194 1 O HIS A 191 N MET A 130 SHEET 4 AA2 5 GLY A 181 ILE A 185 -1 N GLY A 181 O VAL A 194 SHEET 5 AA2 5 TRP A 172 ALA A 176 -1 N LYS A 173 O LYS A 184 SHEET 1 AA3 5 ARG A 108 GLN A 112 0 SHEET 2 AA3 5 MET A 130 MET A 140 -1 O TYR A 137 N ARG A 108 SHEET 3 AA3 5 MET A 196 PRO A 200 1 O TYR A 197 N MET A 138 SHEET 4 AA3 5 ASN A 246 ALA A 248 -1 O ALA A 248 N MET A 196 SHEET 5 AA3 5 TRP A 256 ASN A 258 -1 O ILE A 257 N LEU A 247 LINK OD2 ASP A 131 MG MG A1001 1555 1555 2.34 LINK OD2 ASP A 131 MG MG A1002 1555 1555 2.38 LINK OD2 ASP A 133 MG MG A1001 1555 1555 2.37 LINK MG MG A1001 O2G GTP A1012 1555 1555 2.51 LINK MG MG A1001 O2B GTP A1012 1555 1555 2.36 LINK MG MG A1001 O2A GTP A1012 1555 1555 2.37 LINK MG MG A1001 O HOH A1320 1555 1555 2.32 LINK MG MG A1002 O2A GTP A1012 1555 1555 2.29 LINK MG MG A1002 O3' GTP A1013 1555 1555 2.42 LINK MG MG A1002 O HOH A1322 1555 1555 2.35 LINK MG MG A1002 O HOH A1323 1555 1555 2.42 LINK MG MG A1002 O HOH A1327 1555 1555 2.56 SITE 1 AC1 5 ASP A 131 ASP A 133 MG A1002 GTP A1012 SITE 2 AC1 5 HOH A1320 SITE 1 AC2 7 ASP A 131 MG A1001 GTP A1012 GTP A1013 SITE 2 AC2 7 HOH A1322 HOH A1323 HOH A1327 SITE 1 AC3 7 LYS A 277 HIS A 278 LYS A 281 ASP A 318 SITE 2 AC3 7 ALA A 319 SER A 320 HOH A1110 SITE 1 AC4 6 ALA A 292 GLN A 293 ASN A 394 MET A 395 SITE 2 AC4 6 GLY A 398 HOH A1230 SITE 1 AC5 4 ARG A 290 GLY A 297 GLY A 298 HOH A1271 SITE 1 AC6 5 TRP A 267 ALA A 306 ASN A 310 GLU A 342 SITE 2 AC6 5 PRO A 344 SITE 1 AC7 2 HIS A 317 GLU A 324 SITE 1 AC8 4 GLU A 129 ASP A 291 GTP A1012 HOH A1210 SITE 1 AC9 6 MET A 3 TRP A 5 GLU A 381 SER A 382 SITE 2 AC9 6 ALA A 383 LEU A 409 SITE 1 AD1 6 PHE A 64 TRP A 294 ASP A 295 VAL A 296 SITE 2 AD1 6 HOH A1122 HOH A1203 SITE 1 AD2 8 LEU A 24 LYS A 29 PHE A 115 ASP A 118 SITE 2 AD2 8 LEU A 120 ARG A 284 HOH A1189 HOH A1332 SITE 1 AD3 27 GLN A 112 GLY A 113 SER A 114 TYR A 117 SITE 2 AD3 27 ASP A 131 ASP A 133 PRO A 261 LYS A 287 SITE 3 AD3 27 SER A 301 ASP A 348 LEU A 352 MG A1001 SITE 4 AD3 27 MG A1002 EDO A1008 GTP A1013 HOH A1190 SITE 5 AD3 27 HOH A1206 HOH A1215 HOH A1268 HOH A1292 SITE 6 AD3 27 HOH A1301 HOH A1314 HOH A1321 HOH A1322 SITE 7 AD3 27 HOH A1326 HOH A1327 HOH A1363 SITE 1 AD4 14 GLN A 112 ASP A 131 ASP A 133 LYS A 177 SITE 2 AD4 14 THR A 179 CYS A 180 ARG A 182 ASP A 193 SITE 3 AD4 14 TYR A 197 SER A 259 MG A1002 GTP A1012 SITE 4 AD4 14 HOH A1324 HOH A1352 CRYST1 118.780 49.850 72.860 90.00 93.48 90.00 C 1 2 1 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 0.008419 0.000000 0.000512 0.00000 SCALE2 0.000000 0.020060 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013750 0.00000