HEADER TRANSFERASE 11-JUL-14 4U03 TITLE STRUCTURE OF THE VIBRIO CHOLERAE DI-NUCLEOTIDE CYCLASE (DNCV) IN TITLE 2 COMPLEX WITH GTP AND 5MTHFGLU2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC AMP-GMP SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-419; COMPND 5 SYNONYM: C-AMP-GMP SYNTHASE, DINUCLEOTIDE CYCLASE DNCV; COMPND 6 EC: 2.7.7.86; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE EL TOR N16961; SOURCE 3 ORGANISM_TAXID: 243277; SOURCE 4 GENE: DNCV, VC_0179; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS REGULATION, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.Y.ZHU,Y.XIANG REVDAT 4 08-NOV-23 4U03 1 SOURCE JRNL REMARK LINK REVDAT 3 22-OCT-14 4U03 1 JRNL REVDAT 2 24-SEP-14 4U03 1 JRNL REVDAT 1 17-SEP-14 4U03 0 JRNL AUTH D.ZHU,L.WANG,G.SHANG,X.LIU,J.ZHU,D.LU,L.WANG,B.KAN, JRNL AUTH 2 J.R.ZHANG,Y.XIANG JRNL TITL STRUCTURAL BIOCHEMISTRY OF A VIBRIO CHOLERAE DINUCLEOTIDE JRNL TITL 2 CYCLASE REVEALS CYCLASE ACTIVITY REGULATION BY FOLATES. JRNL REF MOL.CELL V. 55 931 2014 JRNL REFN ISSN 1097-2765 JRNL PMID 25201413 JRNL DOI 10.1016/J.MOLCEL.2014.08.001 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 54229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2754 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 43.6429 - 5.5356 0.96 2597 146 0.1571 0.1777 REMARK 3 2 5.5356 - 4.3951 1.00 2608 154 0.1349 0.1694 REMARK 3 3 4.3951 - 3.8399 1.00 2580 144 0.1438 0.1866 REMARK 3 4 3.8399 - 3.4890 1.00 2614 130 0.1639 0.2288 REMARK 3 5 3.4890 - 3.2390 1.00 2580 150 0.1837 0.2373 REMARK 3 6 3.2390 - 3.0481 1.00 2570 141 0.2005 0.2345 REMARK 3 7 3.0481 - 2.8955 1.00 2585 148 0.2075 0.3012 REMARK 3 8 2.8955 - 2.7695 1.00 2554 154 0.2099 0.2838 REMARK 3 9 2.7695 - 2.6629 1.00 2578 146 0.2120 0.2754 REMARK 3 10 2.6629 - 2.5710 1.00 2578 134 0.2049 0.2589 REMARK 3 11 2.5710 - 2.4906 1.00 2599 110 0.1998 0.2607 REMARK 3 12 2.4906 - 2.4194 1.00 2576 132 0.1913 0.2378 REMARK 3 13 2.4194 - 2.3557 1.00 2581 141 0.1934 0.2868 REMARK 3 14 2.3557 - 2.2983 1.00 2556 141 0.1927 0.2574 REMARK 3 15 2.2983 - 2.2460 1.00 2587 131 0.1980 0.2712 REMARK 3 16 2.2460 - 2.1982 1.00 2569 135 0.2001 0.2740 REMARK 3 17 2.1982 - 2.1543 1.00 2583 148 0.2085 0.2903 REMARK 3 18 2.1543 - 2.1136 1.00 2527 132 0.2099 0.2586 REMARK 3 19 2.1136 - 2.0759 1.00 2608 116 0.2169 0.3008 REMARK 3 20 2.0759 - 2.0407 0.95 2445 121 0.2432 0.3217 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.830 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 6605 REMARK 3 ANGLE : 1.143 8943 REMARK 3 CHIRALITY : 0.070 959 REMARK 3 PLANARITY : 0.004 1134 REMARK 3 DIHEDRAL : 16.258 2551 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 64.2877 8.5722 176.3610 REMARK 3 T TENSOR REMARK 3 T11: 0.2356 T22: 0.1589 REMARK 3 T33: 0.2522 T12: -0.0241 REMARK 3 T13: 0.0045 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.1412 L22: 0.1761 REMARK 3 L33: 1.4644 L12: 0.0367 REMARK 3 L13: -0.1003 L23: -0.1480 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: -0.0400 S13: -0.0020 REMARK 3 S21: 0.0135 S22: -0.0272 S23: -0.0485 REMARK 3 S31: -0.1495 S32: 0.1945 S33: 0.0406 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 4U03 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54229 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 103.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 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: NULL REMARK 200 STARTING MODEL: 4U0L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG 3350, 200MM NACL, 5MM ATP, REMARK 280 5MM GTP, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.92300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 ARG A 2 REMARK 465 VAL A 218 REMARK 465 LYS A 219 REMARK 465 GLY A 220 REMARK 465 ALA A 221 REMARK 465 ILE A 222 REMARK 465 PHE A 223 REMARK 465 GLU A 224 REMARK 465 SER A 225 REMARK 465 TYR A 226 REMARK 465 VAL A 227 REMARK 465 ALA A 228 REMARK 465 ASP A 229 REMARK 465 SER A 230 REMARK 465 ILE A 231 REMARK 465 THR A 232 REMARK 465 ASP A 233 REMARK 465 ASP A 234 REMARK 465 SER A 235 REMARK 465 GLU A 236 REMARK 465 THR A 237 REMARK 465 ALA A 412 REMARK 465 LEU A 413 REMARK 465 PRO A 414 REMARK 465 ALA A 415 REMARK 465 PHE A 416 REMARK 465 ALA A 417 REMARK 465 GLN A 418 REMARK 465 GLU A 419 REMARK 465 LEU A 420 REMARK 465 GLU A 421 REMARK 465 HIS A 422 REMARK 465 HIS A 423 REMARK 465 HIS A 424 REMARK 465 HIS A 425 REMARK 465 HIS A 426 REMARK 465 HIS A 427 REMARK 465 MET B 1 REMARK 465 GLU B 212 REMARK 465 ALA B 213 REMARK 465 ASN B 214 REMARK 465 ARG B 215 REMARK 465 SER B 216 REMARK 465 PHE B 217 REMARK 465 VAL B 218 REMARK 465 LYS B 219 REMARK 465 GLY B 220 REMARK 465 ALA B 221 REMARK 465 ILE B 222 REMARK 465 PHE B 223 REMARK 465 GLU B 224 REMARK 465 SER B 225 REMARK 465 TYR B 226 REMARK 465 VAL B 227 REMARK 465 ALA B 228 REMARK 465 ASP B 229 REMARK 465 SER B 230 REMARK 465 ILE B 231 REMARK 465 THR B 232 REMARK 465 ASP B 233 REMARK 465 ASP B 234 REMARK 465 SER B 235 REMARK 465 GLU B 236 REMARK 465 ALA B 412 REMARK 465 LEU B 413 REMARK 465 PRO B 414 REMARK 465 ALA B 415 REMARK 465 PHE B 416 REMARK 465 ALA B 417 REMARK 465 GLN B 418 REMARK 465 GLU B 419 REMARK 465 LEU B 420 REMARK 465 GLU B 421 REMARK 465 HIS B 422 REMARK 465 HIS B 423 REMARK 465 HIS B 424 REMARK 465 HIS B 425 REMARK 465 HIS B 426 REMARK 465 HIS B 427 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 145 -78.59 -83.41 REMARK 500 SER A 216 -83.14 -118.97 REMARK 500 ASN B 15 -60.74 -93.60 REMARK 500 PHE B 124 -60.62 -109.65 REMARK 500 SER B 145 -78.67 -122.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 692 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 714 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 715 DISTANCE = 8.48 ANGSTROMS REMARK 525 HOH A 720 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 723 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH B 667 DISTANCE = 10.98 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD2 REMARK 620 2 ASP A 133 OD2 85.2 REMARK 620 3 GTP A 501 O3G 95.5 173.4 REMARK 620 4 GTP A 501 O2B 168.4 98.0 82.6 REMARK 620 5 GTP A 501 O2A 88.7 98.7 87.8 79.8 REMARK 620 6 HOH A 750 O 102.7 77.8 95.7 88.8 167.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 ASP A 131 OD2 55.4 REMARK 620 3 ASP A 133 OD1 84.5 87.4 REMARK 620 4 ASP A 193 OD2 96.9 147.4 108.6 REMARK 620 5 GTP A 502 O3' 157.7 120.1 73.3 92.1 REMARK 620 6 HOH A 757 O 116.7 66.0 115.8 125.4 72.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 131 OD2 REMARK 620 2 ASP B 133 OD2 79.7 REMARK 620 3 GTP B 501 O3G 95.8 170.3 REMARK 620 4 GTP B 501 O2B 172.3 102.0 83.6 REMARK 620 5 GTP B 501 O2A 89.4 103.9 84.5 82.9 REMARK 620 6 HOH B 710 O 99.0 78.4 94.0 88.7 171.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 131 OD1 REMARK 620 2 ASP B 131 OD2 46.3 REMARK 620 3 ASP B 133 OD1 76.5 69.5 REMARK 620 4 ASP B 193 OD2 98.2 137.5 132.9 REMARK 620 5 GTP B 502 O3' 151.8 106.4 87.3 109.7 REMARK 620 6 HOH B 714 O 105.2 63.5 103.5 122.7 56.0 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 GTP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLL B 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4U0L RELATED DB: PDB REMARK 900 RELATED ID: 4U0M RELATED DB: PDB REMARK 900 RELATED ID: 4U0N RELATED DB: PDB DBREF 4U03 A 1 419 UNP Q9KVG7 DNCV_VIBCH 1 419 DBREF 4U03 B 1 419 UNP Q9KVG7 DNCV_VIBCH 1 419 SEQADV 4U03 LEU A 420 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 GLU A 421 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS A 422 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS A 423 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS A 424 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS A 425 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS A 426 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS A 427 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 LEU B 420 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 GLU B 421 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS B 422 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS B 423 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS B 424 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS B 425 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS B 426 UNP Q9KVG7 EXPRESSION TAG SEQADV 4U03 HIS B 427 UNP Q9KVG7 EXPRESSION TAG SEQRES 1 A 427 MET ARG MET THR TRP ASN PHE HIS GLN TYR TYR THR ASN SEQRES 2 A 427 ARG ASN ASP GLY LEU MET GLY LYS LEU VAL LEU THR ASP SEQRES 3 A 427 GLU GLU LYS ASN ASN LEU LYS ALA LEU ARG LYS ILE ILE SEQRES 4 A 427 ARG LEU ARG THR ARG ASP VAL PHE GLU GLU ALA LYS GLY SEQRES 5 A 427 ILE ALA LYS ALA VAL LYS LYS SER ALA LEU THR PHE GLU SEQRES 6 A 427 ILE ILE GLN GLU LYS VAL SER THR THR GLN ILE LYS HIS SEQRES 7 A 427 LEU SER ASP SER GLU GLN ARG GLU VAL ALA LYS LEU ILE SEQRES 8 A 427 TYR GLU MET ASP ASP ASP ALA ARG ASP GLU PHE LEU GLY SEQRES 9 A 427 LEU THR PRO ARG PHE TRP THR GLN GLY SER PHE GLN TYR SEQRES 10 A 427 ASP THR LEU ASN ARG PRO PHE GLN PRO GLY GLN GLU MET SEQRES 11 A 427 ASP ILE ASP ASP GLY THR TYR MET PRO MET PRO ILE PHE SEQRES 12 A 427 GLU SER GLU PRO LYS ILE GLY HIS SER LEU LEU ILE LEU SEQRES 13 A 427 LEU VAL ASP ALA SER LEU LYS SER LEU VAL ALA GLU ASN SEQRES 14 A 427 HIS GLY TRP LYS PHE GLU ALA LYS GLN THR CYS GLY ARG SEQRES 15 A 427 ILE LYS ILE GLU ALA GLU LYS THR HIS ILE ASP VAL PRO SEQRES 16 A 427 MET TYR ALA ILE PRO LYS ASP GLU PHE GLN LYS LYS GLN SEQRES 17 A 427 ILE ALA LEU GLU ALA ASN ARG SER PHE VAL LYS GLY ALA SEQRES 18 A 427 ILE PHE GLU SER TYR VAL ALA ASP SER ILE THR ASP ASP SEQRES 19 A 427 SER GLU THR TYR GLU LEU ASP SER GLU ASN VAL ASN LEU SEQRES 20 A 427 ALA LEU ARG GLU GLY ASP ARG LYS TRP ILE ASN SER ASP SEQRES 21 A 427 PRO LYS ILE VAL GLU ASP TRP PHE ASN ASP SER CYS ILE SEQRES 22 A 427 ARG ILE GLY LYS HIS LEU ARG LYS VAL CYS ARG PHE MET SEQRES 23 A 427 LYS ALA TRP ARG ASP ALA GLN TRP ASP VAL GLY GLY PRO SEQRES 24 A 427 SER SER ILE SER LEU MET ALA ALA THR VAL ASN ILE LEU SEQRES 25 A 427 ASP SER VAL ALA HIS ASP ALA SER ASP LEU GLY GLU THR SEQRES 26 A 427 MET LYS ILE ILE ALA LYS HIS LEU PRO SER GLU PHE ALA SEQRES 27 A 427 ARG GLY VAL GLU SER PRO ASP SER THR ASP GLU LYS PRO SEQRES 28 A 427 LEU PHE PRO PRO SER TYR LYS HIS GLY PRO ARG GLU MET SEQRES 29 A 427 ASP ILE MET SER LYS LEU GLU ARG LEU PRO GLU ILE LEU SEQRES 30 A 427 SER SER ALA GLU SER ALA ASP SER LYS SER GLU ALA LEU SEQRES 31 A 427 LYS LYS ILE ASN MET ALA PHE GLY ASN ARG VAL THR ASN SEQRES 32 A 427 SER GLU LEU ILE VAL LEU ALA LYS ALA LEU PRO ALA PHE SEQRES 33 A 427 ALA GLN GLU LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 427 MET ARG MET THR TRP ASN PHE HIS GLN TYR TYR THR ASN SEQRES 2 B 427 ARG ASN ASP GLY LEU MET GLY LYS LEU VAL LEU THR ASP SEQRES 3 B 427 GLU GLU LYS ASN ASN LEU LYS ALA LEU ARG LYS ILE ILE SEQRES 4 B 427 ARG LEU ARG THR ARG ASP VAL PHE GLU GLU ALA LYS GLY SEQRES 5 B 427 ILE ALA LYS ALA VAL LYS LYS SER ALA LEU THR PHE GLU SEQRES 6 B 427 ILE ILE GLN GLU LYS VAL SER THR THR GLN ILE LYS HIS SEQRES 7 B 427 LEU SER ASP SER GLU GLN ARG GLU VAL ALA LYS LEU ILE SEQRES 8 B 427 TYR GLU MET ASP ASP ASP ALA ARG ASP GLU PHE LEU GLY SEQRES 9 B 427 LEU THR PRO ARG PHE TRP THR GLN GLY SER PHE GLN TYR SEQRES 10 B 427 ASP THR LEU ASN ARG PRO PHE GLN PRO GLY GLN GLU MET SEQRES 11 B 427 ASP ILE ASP ASP GLY THR TYR MET PRO MET PRO ILE PHE SEQRES 12 B 427 GLU SER GLU PRO LYS ILE GLY HIS SER LEU LEU ILE LEU SEQRES 13 B 427 LEU VAL ASP ALA SER LEU LYS SER LEU VAL ALA GLU ASN SEQRES 14 B 427 HIS GLY TRP LYS PHE GLU ALA LYS GLN THR CYS GLY ARG SEQRES 15 B 427 ILE LYS ILE GLU ALA GLU LYS THR HIS ILE ASP VAL PRO SEQRES 16 B 427 MET TYR ALA ILE PRO LYS ASP GLU PHE GLN LYS LYS GLN SEQRES 17 B 427 ILE ALA LEU GLU ALA ASN ARG SER PHE VAL LYS GLY ALA SEQRES 18 B 427 ILE PHE GLU SER TYR VAL ALA ASP SER ILE THR ASP ASP SEQRES 19 B 427 SER GLU THR TYR GLU LEU ASP SER GLU ASN VAL ASN LEU SEQRES 20 B 427 ALA LEU ARG GLU GLY ASP ARG LYS TRP ILE ASN SER ASP SEQRES 21 B 427 PRO LYS ILE VAL GLU ASP TRP PHE ASN ASP SER CYS ILE SEQRES 22 B 427 ARG ILE GLY LYS HIS LEU ARG LYS VAL CYS ARG PHE MET SEQRES 23 B 427 LYS ALA TRP ARG ASP ALA GLN TRP ASP VAL GLY GLY PRO SEQRES 24 B 427 SER SER ILE SER LEU MET ALA ALA THR VAL ASN ILE LEU SEQRES 25 B 427 ASP SER VAL ALA HIS ASP ALA SER ASP LEU GLY GLU THR SEQRES 26 B 427 MET LYS ILE ILE ALA LYS HIS LEU PRO SER GLU PHE ALA SEQRES 27 B 427 ARG GLY VAL GLU SER PRO ASP SER THR ASP GLU LYS PRO SEQRES 28 B 427 LEU PHE PRO PRO SER TYR LYS HIS GLY PRO ARG GLU MET SEQRES 29 B 427 ASP ILE MET SER LYS LEU GLU ARG LEU PRO GLU ILE LEU SEQRES 30 B 427 SER SER ALA GLU SER ALA ASP SER LYS SER GLU ALA LEU SEQRES 31 B 427 LYS LYS ILE ASN MET ALA PHE GLY ASN ARG VAL THR ASN SEQRES 32 B 427 SER GLU LEU ILE VAL LEU ALA LYS ALA LEU PRO ALA PHE SEQRES 33 B 427 ALA GLN GLU LEU GLU HIS HIS HIS HIS HIS HIS HET GTP A 501 32 HET GTP A 502 32 HET MG A 503 1 HET MG A 504 1 HET TLL A 505 71 HET GTP B 501 32 HET GTP B 502 32 HET MG B 503 1 HET MG B 504 1 HET TLL B 505 71 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM TLL N-[4-({[(6S)-2-AMINO-5-METHYL-4-OXO-1,4,5,6,7,8- HETNAM 2 TLL HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GAMMA- HETNAM 3 TLL GLUTAMYL-L-GLUTAMIC ACID FORMUL 3 GTP 4(C10 H16 N5 O14 P3) FORMUL 5 MG 4(MG 2+) FORMUL 7 TLL 2(C25 H32 N8 O9) FORMUL 13 HOH *285(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 74 1 12 HELIX 5 AA5 GLN A 75 LEU A 79 5 5 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 ALA A 167 1 18 HELIX 9 AA9 LYS A 201 ASN A 214 1 14 HELIX 10 AB1 ASP A 241 ASN A 244 5 4 HELIX 11 AB2 ASP A 260 GLY A 276 1 17 HELIX 12 AB3 LYS A 277 TRP A 294 1 18 HELIX 13 AB4 SER A 300 VAL A 315 1 16 HELIX 14 AB5 ASP A 321 ARG A 339 1 19 HELIX 15 AB6 PRO A 355 HIS A 359 5 5 HELIX 16 AB7 GLY A 360 SER A 382 1 23 HELIX 17 AB8 SER A 385 GLY A 398 1 14 HELIX 18 AB9 ASN A 403 ILE A 407 5 5 HELIX 19 AC1 PHE B 7 ASN B 13 1 7 HELIX 20 AC2 GLY B 17 VAL B 23 1 7 HELIX 21 AC3 THR B 25 SER B 60 1 36 HELIX 22 AC4 THR B 63 THR B 73 1 11 HELIX 23 AC5 THR B 74 LEU B 79 5 6 HELIX 24 AC6 SER B 80 MET B 94 1 15 HELIX 25 AC7 ASP B 95 LEU B 105 1 11 HELIX 26 AC8 GLY B 150 ALA B 167 1 18 HELIX 27 AC9 LYS B 201 ALA B 210 1 10 HELIX 28 AD1 ASP B 241 ASN B 244 5 4 HELIX 29 AD2 ASP B 260 GLY B 276 1 17 HELIX 30 AD3 LYS B 277 TRP B 294 1 18 HELIX 31 AD4 SER B 300 VAL B 315 1 16 HELIX 32 AD5 ASP B 321 GLY B 340 1 20 HELIX 33 AD6 PRO B 355 HIS B 359 5 5 HELIX 34 AD7 GLY B 360 SER B 382 1 23 HELIX 35 AD8 SER B 385 GLY B 398 1 14 HELIX 36 AD9 ASN B 403 ILE B 407 5 5 SHEET 1 AA1 2 TRP A 5 ASN A 6 0 SHEET 2 AA1 2 VAL A 408 LEU A 409 -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 ASP A 193 N ILE A 132 SHEET 4 AA2 5 GLY A 181 ILE A 185 -1 N ILE A 185 O THR A 190 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 THR A 136 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 SHEET 1 AA4 2 TRP B 5 ASN B 6 0 SHEET 2 AA4 2 VAL B 408 LEU B 409 -1 O VAL B 408 N ASN B 6 SHEET 1 AA5 5 ARG B 108 GLN B 112 0 SHEET 2 AA5 5 MET B 130 MET B 140 -1 O TYR B 137 N ARG B 108 SHEET 3 AA5 5 THR B 190 VAL B 194 1 O ASP B 193 N ILE B 132 SHEET 4 AA5 5 GLY B 181 ILE B 185 -1 N ILE B 185 O THR B 190 SHEET 5 AA5 5 TRP B 172 ALA B 176 -1 N LYS B 173 O LYS B 184 SHEET 1 AA6 5 ARG B 108 GLN B 112 0 SHEET 2 AA6 5 MET B 130 MET B 140 -1 O TYR B 137 N ARG B 108 SHEET 3 AA6 5 MET B 196 PRO B 200 1 O TYR B 197 N MET B 138 SHEET 4 AA6 5 ASN B 246 ALA B 248 -1 O ALA B 248 N MET B 196 SHEET 5 AA6 5 TRP B 256 ASN B 258 -1 O ILE B 257 N LEU B 247 LINK OD2 ASP A 131 MG MG A 503 1555 1555 2.22 LINK OD1 ASP A 131 MG MG A 504 1555 1555 2.57 LINK OD2 ASP A 131 MG MG A 504 1555 1555 2.10 LINK OD2 ASP A 133 MG MG A 503 1555 1555 2.48 LINK OD1 ASP A 133 MG MG A 504 1555 1555 2.25 LINK OD2 ASP A 193 MG MG A 504 1555 1555 2.18 LINK O3G GTP A 501 MG MG A 503 1555 1555 2.22 LINK O2B GTP A 501 MG MG A 503 1555 1555 2.22 LINK O2A GTP A 501 MG MG A 503 1555 1555 2.34 LINK O3' GTP A 502 MG MG A 504 1555 1555 2.01 LINK MG MG A 503 O HOH A 750 1555 1555 2.31 LINK MG MG A 504 O HOH A 757 1555 1555 2.89 LINK OD2 ASP B 131 MG MG B 503 1555 1555 2.52 LINK OD1 ASP B 131 MG MG B 504 1555 1555 2.99 LINK OD2 ASP B 131 MG MG B 504 1555 1555 2.53 LINK OD2 ASP B 133 MG MG B 503 1555 1555 2.38 LINK OD1 ASP B 133 MG MG B 504 1555 1555 2.38 LINK OD2 ASP B 193 MG MG B 504 1555 1555 1.91 LINK O3G GTP B 501 MG MG B 503 1555 1555 2.49 LINK O2B GTP B 501 MG MG B 503 1555 1555 2.19 LINK O2A GTP B 501 MG MG B 503 1555 1555 2.24 LINK O3' GTP B 502 MG MG B 504 1555 1555 2.10 LINK MG MG B 503 O HOH B 710 1555 1555 2.43 LINK MG MG B 504 O HOH B 714 1555 1555 2.72 SITE 1 AC1 22 GLN A 112 GLY A 113 SER A 114 TYR A 117 SITE 2 AC1 22 ASP A 131 ASP A 133 LYS A 287 SER A 301 SITE 3 AC1 22 ASP A 345 ASP A 348 LEU A 352 GTP A 502 SITE 4 AC1 22 MG A 503 HOH A 643 HOH A 658 HOH A 663 SITE 5 AC1 22 HOH A 665 HOH A 680 HOH A 691 HOH A 742 SITE 6 AC1 22 HOH A 748 HOH A 757 SITE 1 AC2 14 GLN A 112 ASP A 131 ASP A 133 LYS A 177 SITE 2 AC2 14 THR A 179 CYS A 180 ARG A 182 ASP A 193 SITE 3 AC2 14 TYR A 197 LEU A 247 SER A 259 GTP A 501 SITE 4 AC2 14 MG A 504 HOH A 757 SITE 1 AC3 4 ASP A 131 ASP A 133 GTP A 501 HOH A 750 SITE 1 AC4 5 ASP A 131 ASP A 133 ASP A 193 GTP A 502 SITE 2 AC4 5 HOH A 757 SITE 1 AC5 17 ARG A 36 ARG A 40 ARG A 44 ARG A 108 SITE 2 AC5 17 PHE A 109 TRP A 110 THR A 111 GLN A 116 SITE 3 AC5 17 TYR A 137 PHE A 204 GLN A 208 TYR A 238 SITE 4 AC5 17 GLU A 239 LEU A 240 ASP A 260 PRO A 261 SITE 5 AC5 17 LYS A 262 SITE 1 AC6 23 GLN B 112 GLY B 113 SER B 114 TYR B 117 SITE 2 AC6 23 ASP B 131 ASP B 133 LYS B 287 ARG B 290 SITE 3 AC6 23 SER B 301 ASP B 345 ASP B 348 LEU B 352 SITE 4 AC6 23 GTP B 502 MG B 503 HOH B 630 HOH B 633 SITE 5 AC6 23 HOH B 688 HOH B 689 HOH B 691 HOH B 692 SITE 6 AC6 23 HOH B 700 HOH B 706 HOH B 714 SITE 1 AC7 14 GLN B 112 ASP B 133 LYS B 177 THR B 179 SITE 2 AC7 14 CYS B 180 ARG B 182 ASP B 193 TYR B 197 SITE 3 AC7 14 SER B 259 GTP B 501 MG B 504 HOH B 653 SITE 4 AC7 14 HOH B 665 HOH B 714 SITE 1 AC8 4 ASP B 131 ASP B 133 GTP B 501 HOH B 710 SITE 1 AC9 5 ASP B 131 ASP B 133 ASP B 193 GTP B 502 SITE 2 AC9 5 HOH B 714 SITE 1 AD1 16 ARG B 36 ARG B 40 ARG B 108 PHE B 109 SITE 2 AD1 16 TRP B 110 THR B 111 GLN B 116 TYR B 137 SITE 3 AD1 16 PHE B 204 TYR B 238 GLU B 239 LEU B 240 SITE 4 AD1 16 SER B 242 ASP B 260 PRO B 261 LYS B 262 CRYST1 69.623 59.846 104.053 90.00 95.81 90.00 P 1 21 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 0.014363 0.000000 0.001461 0.00000 SCALE2 0.000000 0.016710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009660 0.00000