HEADER TRANSFERASE 08-JAN-15 4XJ5 TITLE CRYSTAL STRUCTURE OF VIBRIO CHOLERAE DNCV 3'-DEOXY 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 4XJ5 1 LINK REVDAT 3 05-FEB-20 4XJ5 1 SOURCE JRNL REMARK REVDAT 2 20-MAY-15 4XJ5 1 JRNL REVDAT 1 29-APR-15 4XJ5 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 60174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 3018 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 47.0190 - 4.3470 0.94 2596 139 0.1660 0.1595 REMARK 3 2 4.3470 - 3.4507 0.99 2652 137 0.1502 0.1642 REMARK 3 3 3.4507 - 3.0146 1.00 2648 136 0.1692 0.1968 REMARK 3 4 3.0146 - 2.7390 1.00 2651 142 0.1848 0.1706 REMARK 3 5 2.7390 - 2.5427 1.00 2623 144 0.1714 0.1890 REMARK 3 6 2.5427 - 2.3928 1.00 2647 131 0.1736 0.1927 REMARK 3 7 2.3928 - 2.2729 1.00 2615 132 0.1685 0.1888 REMARK 3 8 2.2729 - 2.1740 1.00 2632 140 0.1651 0.1828 REMARK 3 9 2.1740 - 2.0903 1.00 2619 146 0.1657 0.2098 REMARK 3 10 2.0903 - 2.0182 1.00 2654 127 0.1705 0.1728 REMARK 3 11 2.0182 - 1.9551 0.99 2565 147 0.1787 0.2600 REMARK 3 12 1.9551 - 1.8992 1.00 2652 132 0.1834 0.2360 REMARK 3 13 1.8992 - 1.8492 1.00 2611 145 0.1938 0.2355 REMARK 3 14 1.8492 - 1.8041 1.00 2629 129 0.1988 0.2257 REMARK 3 15 1.8041 - 1.7631 1.00 2621 146 0.2010 0.2546 REMARK 3 16 1.7631 - 1.7255 1.00 2604 132 0.2066 0.2365 REMARK 3 17 1.7255 - 1.6910 1.00 2613 137 0.2064 0.2471 REMARK 3 18 1.6910 - 1.6591 1.00 2632 152 0.2106 0.2635 REMARK 3 19 1.6591 - 1.6295 1.00 2600 119 0.2190 0.2499 REMARK 3 20 1.6295 - 1.6018 0.99 2592 143 0.2475 0.2393 REMARK 3 21 1.6018 - 1.5760 0.94 2466 133 0.2587 0.2852 REMARK 3 22 1.5760 - 1.5518 0.85 2234 129 0.3052 0.3529 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.460 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 : 0.012 3119 REMARK 3 ANGLE : 1.338 4221 REMARK 3 CHIRALITY : 0.061 460 REMARK 3 PLANARITY : 0.006 542 REMARK 3 DIHEDRAL : 12.487 1158 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): 41.4580 28.2158 70.4240 REMARK 3 T TENSOR REMARK 3 T11: 0.3676 T22: 0.3368 REMARK 3 T33: 0.1971 T12: -0.1082 REMARK 3 T13: -0.0174 T23: 0.0349 REMARK 3 L TENSOR REMARK 3 L11: 1.1142 L22: 2.3105 REMARK 3 L33: 5.3438 L12: 1.4009 REMARK 3 L13: -2.5534 L23: -3.9276 REMARK 3 S TENSOR REMARK 3 S11: 0.2026 S12: -0.2951 S13: -0.1145 REMARK 3 S21: 0.3881 S22: -0.2656 S23: -0.0374 REMARK 3 S31: -0.5192 S32: 0.4677 S33: 0.0412 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 94 THROUGH 293 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.8756 24.1766 62.6597 REMARK 3 T TENSOR REMARK 3 T11: 0.2664 T22: 0.2518 REMARK 3 T33: 0.2325 T12: -0.0272 REMARK 3 T13: -0.0177 T23: 0.0654 REMARK 3 L TENSOR REMARK 3 L11: 0.4599 L22: 0.8731 REMARK 3 L33: 3.1133 L12: 0.4727 REMARK 3 L13: -0.8978 L23: -1.5226 REMARK 3 S TENSOR REMARK 3 S11: 0.0144 S12: -0.2480 S13: -0.1959 REMARK 3 S21: 0.2412 S22: -0.1012 S23: -0.0274 REMARK 3 S31: 0.0001 S32: 0.1978 S33: 0.0848 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 294 THROUGH 412 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.4165 35.0776 38.2762 REMARK 3 T TENSOR REMARK 3 T11: 0.1438 T22: 0.1711 REMARK 3 T33: 0.1394 T12: 0.0111 REMARK 3 T13: -0.0257 T23: -0.0168 REMARK 3 L TENSOR REMARK 3 L11: 1.9950 L22: 1.7675 REMARK 3 L33: 0.9430 L12: 1.1415 REMARK 3 L13: -0.4350 L23: -0.3063 REMARK 3 S TENSOR REMARK 3 S11: 0.0380 S12: 0.0942 S13: -0.0558 REMARK 3 S21: 0.0034 S22: -0.0393 S23: 0.0524 REMARK 3 S31: 0.0328 S32: -0.0719 S33: 0.0007 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 4XJ5 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_1000205775. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5-7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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 : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60205 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 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: SAD 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 (%): 48.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 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 58.97500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.03000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.97500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.03000 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: 980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 PHE A 143 REMARK 465 GLU A 144 REMARK 465 SER A 145 REMARK 465 GLU A 146 REMARK 465 PRO A 147 REMARK 465 ASP A 202 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 LYS A 77 CG CD CE NZ REMARK 470 ARG A 108 CZ NH1 NH2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 HIS A 170 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 GLU A 243 CG CD OE1 OE2 REMARK 470 GLU A 251 CG CD OE1 OE2 REMARK 470 ASP A 253 CG OD1 OD2 REMARK 470 LYS A 262 CG CD CE NZ REMARK 470 LYS A 350 CG CD CE NZ REMARK 470 LYS A 391 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 OE1 GLN A 9 O HOH A 1101 1.78 REMARK 500 O HOH A 1263 O HOH A 1296 1.96 REMARK 500 NH1 ARG A 99 O HOH A 1102 2.08 REMARK 500 O HOH A 1210 O HOH A 1327 2.13 REMARK 500 OG SER A 335 O HOH A 1340 2.16 REMARK 500 O ASN A 258 O HOH A 1332 2.17 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 ASN A 15 -70.34 -77.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GH3 A 1013 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 86.7 REMARK 620 3 GH3 A1014 O3G 94.0 179.1 REMARK 620 4 GH3 A1014 O2B 175.7 94.7 84.7 REMARK 620 5 GH3 A1014 O2A 89.9 92.6 88.1 86.0 REMARK 620 6 HOH A1282 O 102.9 84.7 94.4 81.3 166.7 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 OD1 REMARK 620 2 ASP A 131 OD2 56.3 REMARK 620 3 ASP A 133 OD1 113.4 87.9 REMARK 620 4 ASP A 193 OD2 95.0 150.4 113.2 REMARK 620 5 HOH A1303 O 117.9 87.6 113.6 101.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1015 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 369 O REMARK 620 2 HOH A1181 O 111.0 REMARK 620 N 1 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 EDO A 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GH3 A 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GH3 A 1014 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 1015 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XJ1 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ3 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ4 RELATED DB: PDB REMARK 900 RELATED ID: 4XJ6 RELATED DB: PDB DBREF 4XJ5 A 1 215 UNP Q9KVG7 DNCV_VIBCH 1 215 DBREF 4XJ5 A 242 412 UNP Q9KVG7 DNCV_VIBCH 242 412 SEQADV 4XJ5 GLY A 239 UNP Q9KVG7 LINKER SEQADV 4XJ5 SER A 240 UNP Q9KVG7 LINKER SEQADV 4XJ5 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 EDO A1012 4 HET GH3 A1013 23 HET GH3 A1014 31 HET NA A1015 1 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GH3 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG 2(MG 2+) FORMUL 4 EDO 10(C2 H6 O2) FORMUL 14 GH3 2(C10 H16 N5 O13 P3) FORMUL 16 NA NA 1+ FORMUL 17 HOH *240(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 113 GLN A 116 5 4 HELIX 9 AA9 GLY A 150 ASN A 169 1 20 HELIX 10 AB1 GLY 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 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 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 ILE A 199 N MET A 140 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 1.98 LINK OD1 ASP A 131 MG MG A1002 1555 1555 2.33 LINK OD2 ASP A 131 MG MG A1002 1555 1555 2.31 LINK OD2 ASP A 133 MG MG A1001 1555 1555 2.15 LINK OD1 ASP A 133 MG MG A1002 1555 1555 2.24 LINK OD2 ASP A 193 MG MG A1002 1555 1555 2.12 LINK O LYS A 369 NA NA A1015 1555 1555 2.79 LINK MG MG A1001 O3G GH3 A1014 1555 1555 2.17 LINK MG MG A1001 O2B GH3 A1014 1555 1555 2.17 LINK MG MG A1001 O2A GH3 A1014 1555 1555 2.11 LINK MG MG A1001 O HOH A1282 1555 1555 2.03 LINK MG MG A1002 O HOH A1303 1555 1555 2.20 LINK NA NA A1015 O HOH A1181 1555 1555 2.80 SITE 1 AC1 4 ASP A 131 ASP A 133 GH3 A1014 HOH A1282 SITE 1 AC2 6 ASP A 131 ASP A 133 ASP A 193 GH3 A1013 SITE 2 AC2 6 GH3 A1014 HOH A1303 SITE 1 AC3 5 ALA A 292 ASN A 394 MET A 395 GLY A 398 SITE 2 AC3 5 HOH A1221 SITE 1 AC4 6 GLY A 297 GLY A 298 SER A 300 HOH A1127 SITE 2 AC4 6 HOH A1188 HOH A1253 SITE 1 AC5 3 LYS A 277 ALA A 316 GLU A 324 SITE 1 AC6 5 MET A 3 TRP A 5 GLU A 381 SER A 382 SITE 2 AC6 5 ALA A 383 SITE 1 AC7 8 PHE A 64 TRP A 294 ASP A 295 VAL A 296 SITE 2 AC7 8 HOH A1116 HOH A1120 HOH A1141 HOH A1197 SITE 1 AC8 8 LYS A 29 SER A 114 PHE A 115 ASP A 118 SITE 2 AC8 8 THR A 119 LEU A 120 ARG A 284 HOH A1183 SITE 1 AC9 1 ARG A 108 SITE 1 AD1 4 SER A 314 HIS A 332 GLU A 336 HOH A1340 SITE 1 AD2 6 PHE A 7 TYR A 11 GLY A 323 LEU A 377 SITE 2 AD2 6 GLU A 381 ILE A 393 SITE 1 AD3 8 LYS A 277 HIS A 317 ASP A 318 ALA A 319 SITE 2 AD3 8 HOH A1106 HOH A1132 HOH A1137 HOH A1256 SITE 1 AD4 10 GLN A 112 ASP A 133 LYS A 177 THR A 179 SITE 2 AD4 10 CYS A 180 ASP A 193 TYR A 197 SER A 259 SITE 3 AD4 10 MG A1002 GH3 A1014 SITE 1 AD5 24 GLN A 112 GLY A 113 SER A 114 TYR A 117 SITE 2 AD5 24 ASP A 131 ASP A 133 LYS A 287 SER A 301 SITE 3 AD5 24 ASP A 348 LEU A 352 MG A1001 MG A1002 SITE 4 AD5 24 GH3 A1013 HOH A1184 HOH A1199 HOH A1207 SITE 5 AD5 24 HOH A1250 HOH A1272 HOH A1279 HOH A1282 SITE 6 AD5 24 HOH A1283 HOH A1284 HOH A1286 HOH A1303 SITE 1 AD6 5 TRP A 289 LYS A 369 LEU A 373 ILE A 376 SITE 2 AD6 5 HOH A1181 CRYST1 117.950 50.060 72.270 90.00 93.40 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 0.008478 0.000000 0.000504 0.00000 SCALE2 0.000000 0.019976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013861 0.00000