HEADER TRANSCRIPTION 08-AUG-21 7V2B TITLE CRYSTAL STRUCTURE OF VPSR DISPLAY NOVEL DIMERIC ARCHITECTURE AND C-DI- TITLE 2 GMP BINDING: MECHANISTIC IMPLICATIONS IN OLIGOMERIZATION, ATPASE TITLE 3 ACTIVITY AND DNA BINDING. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VPSR; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: VPSR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A+ KEYWDS X-RAY CRYSTALLOGRAPHY; BIOFILM; FLUORESCENCE QUENCHING; ATPASE KEYWDS 2 ACTIVITY; SECOND-MESSENGER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.CHAKRABORTTY,U.SEN REVDAT 2 29-NOV-23 7V2B 1 REMARK REVDAT 1 06-APR-22 7V2B 0 JRNL AUTH T.CHAKRABORTTY,S.ROY CHOWDHURY,B.GHOSH,U.SEN JRNL TITL CRYSTAL STRUCTURE OF VPSR REVEALED NOVEL DIMERIC JRNL TITL 2 ARCHITECTURE AND C-DI-GMP BINDING SITE: MECHANISTIC JRNL TITL 3 IMPLICATIONS IN OLIGOMERIZATION, ATPASE ACTIVITY AND DNA JRNL TITL 4 BINDING. JRNL REF J.MOL.BIOL. V. 434 67354 2022 JRNL REFN ESSN 1089-8638 JRNL PMID 34774564 JRNL DOI 10.1016/J.JMB.2021.167354 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 20381 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 3615 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 47.2730 - 9.4556 0.89 1232 147 0.1345 0.1666 REMARK 3 2 9.4556 - 7.5150 0.86 1223 130 0.1502 0.2050 REMARK 3 3 7.5150 - 6.5679 0.94 1323 156 0.2053 0.2879 REMARK 3 4 6.5679 - 5.9686 0.90 1243 139 0.2379 0.2926 REMARK 3 5 5.9686 - 5.5415 0.88 1272 137 0.2475 0.3138 REMARK 3 6 5.5415 - 5.2152 0.92 1254 143 0.2278 0.2802 REMARK 3 7 5.2152 - 4.9544 0.92 1309 134 0.2024 0.2275 REMARK 3 8 4.9544 - 4.7389 0.93 1276 152 0.1917 0.2721 REMARK 3 9 4.7389 - 4.5566 0.88 1235 124 0.2028 0.2765 REMARK 3 10 4.5566 - 4.3995 0.88 1258 153 0.1999 0.2630 REMARK 3 11 4.3995 - 4.2620 0.88 1260 128 0.2203 0.2808 REMARK 3 12 4.2620 - 4.1403 0.90 1263 139 0.2359 0.3253 REMARK 3 13 4.1403 - 4.0313 0.91 1290 116 0.2590 0.3062 REMARK 3 14 4.0313 - 3.9330 0.94 1320 142 0.2522 0.2692 REMARK 3 15 3.9330 - 3.8437 0.91 1261 144 0.2686 0.3652 REMARK 3 16 3.8437 - 3.7619 0.93 1350 136 0.2966 0.3264 REMARK 3 17 3.7619 - 3.6867 0.88 1259 145 0.2997 0.3679 REMARK 3 18 3.6867 - 3.6171 0.91 1270 148 0.2793 0.3560 REMARK 3 19 3.6171 - 3.5526 0.86 1165 126 0.2841 0.3330 REMARK 3 20 3.5526 - 3.4924 0.88 1284 121 0.2836 0.2894 REMARK 3 21 3.4924 - 3.4360 0.92 1264 142 0.2865 0.3532 REMARK 3 22 3.4360 - 3.3832 0.91 1238 132 0.3097 0.3603 REMARK 3 23 3.3832 - 3.3334 0.91 1353 166 0.3720 0.3654 REMARK 3 24 3.3334 - 3.2865 0.93 1299 141 0.3948 0.4615 REMARK 3 25 3.2865 - 3.2421 0.91 1300 131 0.4041 0.4512 REMARK 3 26 3.2421 - 3.2000 0.92 1296 143 0.4429 0.4384 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) : 0.560 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.390 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 : 0.004 6063 REMARK 3 ANGLE : 1.050 8223 REMARK 3 CHIRALITY : 0.038 937 REMARK 3 PLANARITY : 0.004 1051 REMARK 3 DIHEDRAL : 17.041 2271 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 8 THROUGH 113 ) REMARK 3 ORIGIN FOR THE GROUP (A): -97.5486 28.7251 5.1443 REMARK 3 T TENSOR REMARK 3 T11: 0.8213 T22: 1.0516 REMARK 3 T33: 1.4370 T12: -0.2063 REMARK 3 T13: -0.2125 T23: -0.2279 REMARK 3 L TENSOR REMARK 3 L11: 8.4876 L22: 8.5055 REMARK 3 L33: 8.7334 L12: -2.1684 REMARK 3 L13: -3.6383 L23: -3.3451 REMARK 3 S TENSOR REMARK 3 S11: 0.2471 S12: -0.8963 S13: 0.6000 REMARK 3 S21: 0.4373 S22: 0.1370 S23: 0.4536 REMARK 3 S31: -0.6147 S32: 0.4713 S33: -0.2593 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 114 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A):-109.4328 18.7506 -4.8240 REMARK 3 T TENSOR REMARK 3 T11: 1.3587 T22: 1.1997 REMARK 3 T33: 2.1851 T12: -0.2975 REMARK 3 T13: 0.0188 T23: 0.2368 REMARK 3 L TENSOR REMARK 3 L11: 2.1304 L22: 4.4662 REMARK 3 L33: -0.1879 L12: 0.7320 REMARK 3 L13: -0.1387 L23: 0.6261 REMARK 3 S TENSOR REMARK 3 S11: 0.3095 S12: -0.6827 S13: 1.8510 REMARK 3 S21: 1.2223 S22: 0.1473 S23: 3.2837 REMARK 3 S31: -0.0365 S32: 0.0943 S33: -0.2196 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 165 THROUGH 382 ) REMARK 3 ORIGIN FOR THE GROUP (A):-100.3987 -0.8577 -18.2839 REMARK 3 T TENSOR REMARK 3 T11: 1.0077 T22: 1.0221 REMARK 3 T33: 1.0728 T12: -0.2218 REMARK 3 T13: -0.3537 T23: 0.2202 REMARK 3 L TENSOR REMARK 3 L11: 2.4461 L22: 4.6389 REMARK 3 L33: 3.3921 L12: 1.1176 REMARK 3 L13: -2.1043 L23: -1.0178 REMARK 3 S TENSOR REMARK 3 S11: -0.2864 S12: 0.2154 S13: 0.0928 REMARK 3 S21: -0.3252 S22: 0.1079 S23: 0.2480 REMARK 3 S31: 0.2776 S32: 0.0451 S33: 0.1601 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 7 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): -97.4887 41.8541 -24.3946 REMARK 3 T TENSOR REMARK 3 T11: 1.6085 T22: 1.0233 REMARK 3 T33: 2.0583 T12: -0.2117 REMARK 3 T13: -0.1259 T23: 0.3210 REMARK 3 L TENSOR REMARK 3 L11: 4.5522 L22: 4.4908 REMARK 3 L33: 7.0131 L12: -4.2928 REMARK 3 L13: -4.7003 L23: 4.6644 REMARK 3 S TENSOR REMARK 3 S11: 0.5048 S12: 1.0890 S13: -1.0260 REMARK 3 S21: -1.4659 S22: 0.4923 S23: 0.8998 REMARK 3 S31: -1.2050 S32: 0.4348 S33: -0.7908 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 43 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): -94.8920 29.6087 -22.1321 REMARK 3 T TENSOR REMARK 3 T11: 1.0841 T22: 1.1622 REMARK 3 T33: 1.9952 T12: -0.3015 REMARK 3 T13: -0.4593 T23: 0.2195 REMARK 3 L TENSOR REMARK 3 L11: 3.9458 L22: 6.1459 REMARK 3 L33: 9.0103 L12: 4.7421 REMARK 3 L13: -0.4207 L23: 1.9473 REMARK 3 S TENSOR REMARK 3 S11: 0.5903 S12: -0.3490 S13: -0.1456 REMARK 3 S21: -0.7783 S22: -0.1456 S23: -0.0273 REMARK 3 S31: 0.0062 S32: 0.3872 S33: -0.8103 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 84 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A):-103.2936 35.1643 -14.3403 REMARK 3 T TENSOR REMARK 3 T11: 1.0427 T22: 1.0912 REMARK 3 T33: 1.8974 T12: -0.2388 REMARK 3 T13: -0.2580 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 2.8632 L22: 5.3398 REMARK 3 L33: 2.6770 L12: 3.0296 REMARK 3 L13: -0.3074 L23: 0.0940 REMARK 3 S TENSOR REMARK 3 S11: 0.1432 S12: -0.0140 S13: 1.1920 REMARK 3 S21: -0.0136 S22: 0.5900 S23: 1.6571 REMARK 3 S31: -0.4295 S32: -0.1680 S33: -0.3779 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 134 THROUGH 207 ) REMARK 3 ORIGIN FOR THE GROUP (A): -73.5111 17.7042 -5.9380 REMARK 3 T TENSOR REMARK 3 T11: 0.8681 T22: 1.5778 REMARK 3 T33: 1.4928 T12: -0.1147 REMARK 3 T13: -0.2421 T23: -0.0764 REMARK 3 L TENSOR REMARK 3 L11: 3.6228 L22: 2.8080 REMARK 3 L33: 3.8959 L12: 0.2918 REMARK 3 L13: -0.8656 L23: -0.0423 REMARK 3 S TENSOR REMARK 3 S11: -0.3092 S12: -0.4972 S13: 0.2673 REMARK 3 S21: 0.2206 S22: 0.1434 S23: -1.0071 REMARK 3 S31: -0.3118 S32: 0.7323 S33: 0.3657 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 208 THROUGH 382 ) REMARK 3 ORIGIN FOR THE GROUP (A): -68.6006 8.1199 -0.5686 REMARK 3 T TENSOR REMARK 3 T11: 0.7398 T22: 1.5420 REMARK 3 T33: 1.2735 T12: 0.0431 REMARK 3 T13: -0.2574 T23: -0.1725 REMARK 3 L TENSOR REMARK 3 L11: 2.0572 L22: 2.5059 REMARK 3 L33: 2.7540 L12: -0.6280 REMARK 3 L13: -1.7498 L23: 1.0440 REMARK 3 S TENSOR REMARK 3 S11: -0.2776 S12: -0.8925 S13: -0.2762 REMARK 3 S21: -0.0419 S22: 0.4942 S23: -0.3660 REMARK 3 S31: 0.5004 S32: 0.8747 S33: -0.4119 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 7V2B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1300023803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8-8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97242 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 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65219 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 47.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 1.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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: 1NY5 REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS REMARK 200 AND I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMS(0.8M) BICENE PH 8.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.08500 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.17000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 GLN A 4 REMARK 465 PHE A 5 REMARK 465 ARG A 6 REMARK 465 MET A 7 REMARK 465 HIS D -16 REMARK 465 HIS D -15 REMARK 465 HIS D -14 REMARK 465 HIS D -13 REMARK 465 HIS D -12 REMARK 465 HIS D -11 REMARK 465 SER D -10 REMARK 465 SER D -9 REMARK 465 GLY D -8 REMARK 465 LEU D -7 REMARK 465 VAL D -6 REMARK 465 PRO D -5 REMARK 465 ARG D -4 REMARK 465 GLY D -3 REMARK 465 SER D -2 REMARK 465 HIS D -1 REMARK 465 MET D 0 REMARK 465 MET D 1 REMARK 465 SER D 2 REMARK 465 THR D 3 REMARK 465 GLN D 4 REMARK 465 PHE D 5 REMARK 465 ARG D 6 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 ASP A 8 CG OD1 OD2 REMARK 470 MET D 7 CG SD CE REMARK 470 ASP D 8 CG OD1 OD2 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 OD2 ASP D 376 OG SER D 378 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU D 130 CA - CB - CG ANGL. DEV. = 14.0 DEGREES 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 TYR A 21 36.95 -79.85 REMARK 500 PRO A 23 -41.47 -11.10 REMARK 500 SER A 61 -144.66 50.73 REMARK 500 ASP A 63 -112.80 -77.34 REMARK 500 SER A 76 72.92 -65.71 REMARK 500 ARG A 81 3.18 -67.03 REMARK 500 GLN A 90 -39.02 -24.86 REMARK 500 SER A 92 -118.53 -76.09 REMARK 500 SER A 93 -142.53 61.90 REMARK 500 ASP A 94 -67.92 27.23 REMARK 500 PHE A 103 -73.83 44.23 REMARK 500 CYS A 104 2.43 59.88 REMARK 500 ILE A 105 -61.03 50.23 REMARK 500 PRO A 136 11.00 -64.07 REMARK 500 PHE A 138 97.17 49.46 REMARK 500 ALA A 141 -83.26 61.48 REMARK 500 ASN A 143 69.37 -65.50 REMARK 500 MET A 144 -15.06 65.39 REMARK 500 LEU A 146 17.12 36.73 REMARK 500 ILE A 147 -67.49 -161.62 REMARK 500 GLU A 149 112.78 -171.63 REMARK 500 SER A 150 -99.11 -135.50 REMARK 500 MET A 151 -41.53 -146.88 REMARK 500 ALA A 205 42.37 -98.57 REMARK 500 SER A 213 23.81 -74.87 REMARK 500 LEU A 218 -99.02 -125.99 REMARK 500 GLU A 220 87.91 -65.22 REMARK 500 GLU A 222 81.36 56.54 REMARK 500 ASP A 241 72.59 51.61 REMARK 500 ASP A 282 104.58 -58.30 REMARK 500 ARG A 313 68.36 -100.45 REMARK 500 ASN A 333 11.23 57.97 REMARK 500 TRP A 352 79.05 57.00 REMARK 500 ASN A 355 -129.16 54.14 REMARK 500 LEU A 380 -91.63 -86.03 REMARK 500 TYR D 21 40.84 -77.40 REMARK 500 PRO D 23 -39.48 -9.21 REMARK 500 SER D 61 -146.23 48.96 REMARK 500 ASP D 63 -111.04 -78.79 REMARK 500 PHE D 65 138.04 69.47 REMARK 500 HIS D 77 0.09 -165.60 REMARK 500 VAL D 80 -35.51 -134.49 REMARK 500 ARG D 81 51.39 -69.95 REMARK 500 TRP D 82 -46.70 -151.25 REMARK 500 LEU D 83 106.22 40.76 REMARK 500 SER D 92 88.04 -58.17 REMARK 500 SER D 93 -82.94 -161.36 REMARK 500 ASP D 94 -134.37 -85.11 REMARK 500 ILE D 96 -37.61 -30.49 REMARK 500 ASN D 102 58.20 -69.09 REMARK 500 REMARK 500 THIS ENTRY HAS 77 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 7V2B A 1 382 UNP Q9AQ41 Q9AQ41_VIBCL 1 382 DBREF 7V2B D 1 382 UNP Q9AQ41 Q9AQ41_VIBCL 1 382 SEQADV 7V2B HIS A -16 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS A -15 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS A -14 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS A -13 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS A -12 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS A -11 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B SER A -10 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B SER A -9 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B GLY A -8 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B LEU A -7 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B VAL A -6 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B PRO A -5 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B ARG A -4 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B GLY A -3 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B SER A -2 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS A -1 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B MET A 0 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS D -16 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS D -15 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS D -14 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS D -13 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS D -12 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS D -11 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B SER D -10 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B SER D -9 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B GLY D -8 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B LEU D -7 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B VAL D -6 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B PRO D -5 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B ARG D -4 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B GLY D -3 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B SER D -2 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B HIS D -1 UNP Q9AQ41 EXPRESSION TAG SEQADV 7V2B MET D 0 UNP Q9AQ41 EXPRESSION TAG SEQRES 1 A 399 HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO ARG SEQRES 2 A 399 GLY SER HIS MET MET SER THR GLN PHE ARG MET ASP SER SEQRES 3 A 399 VAL PRO GLY SER LEU VAL VAL VAL GLY GLY THR TYR GLU SEQRES 4 A 399 PRO TRP LEU PRO VAL LEU GLU LYS VAL GLY TRP ARG CYS SEQRES 5 A 399 THR GLN VAL ALA ASP LEU ARG LYS PRO ASP ALA LEU PHE SEQRES 6 A 399 VAL GLU THR GLY PRO CYS ILE GLY ILE VAL ASP LEU SER SEQRES 7 A 399 HIS ASP GLU PHE SER LEU ASN GLY ILE ALA ASN LEU VAL SEQRES 8 A 399 SER SER HIS LYS GLN VAL ARG TRP LEU ALA PHE ILE ARG SEQRES 9 A 399 GLU ALA GLN LEU SER SER ASP THR ILE CYS GLN PHE ILE SEQRES 10 A 399 VAL ASN PHE CYS ILE ASP PHE PHE THR ALA PRO ILE PRO SEQRES 11 A 399 ASP ALA GLN LEU LEU SER THR ILE GLY HIS GLN LEU GLY SEQRES 12 A 399 MET LEU LYS LEU GLU LYS LYS VAL TRP PRO HIS PHE GLY SEQRES 13 A 399 SER ALA GLY ASN MET GLY LEU ILE GLY GLU SER MET PRO SEQRES 14 A 399 MET LYS ARG LEU ARG ASP GLN ILE LYS ARG ILE GLY PRO SEQRES 15 A 399 THR ASP VAL SER ILE LEU ILE TYR GLY GLU SER GLY THR SEQRES 16 A 399 GLY LYS GLU THR VAL ALA LYS ALA ILE HIS LYS THR SER SEQRES 17 A 399 SER ARG ALA GLN LYS PRO PHE ILE SER VAL ASN CYS ARG SEQRES 18 A 399 ALA MET SER GLU LYS ARG LEU GLU SER GLU LEU PHE GLY SEQRES 19 A 399 LEU GLY GLU THR GLU GLU GLY GLN GLN PRO PHE LEU LEU SEQRES 20 A 399 GLN ALA ASP GLY GLY THR LEU LEU LEU ASN ASP ILE LEU SEQRES 21 A 399 THR LEU PRO LYS SER GLN GLN LEU ASN LEU LEU ARG PHE SEQRES 22 A 399 LEU GLN GLU GLY THR VAL GLU THR ARG GLN GLY VAL ARG SEQRES 23 A 399 ALA VAL ASP VAL ARG ILE LEU ALA ALA ASN SER SER ASP SEQRES 24 A 399 ILE GLU LYS ALA LEU ILE ASP GLY ASP PHE ASN GLU GLU SEQRES 25 A 399 LEU TYR HIS TYR ILE ASN VAL LEU ARG ILE ASN VAL PRO SEQRES 26 A 399 SER LEU LYS GLU ARG ALA SER ASP ILE VAL LEU LEU ALA SEQRES 27 A 399 LYS HIS PHE LEU GLN GLU TYR SER LYS GLU TYR ASN ALA SEQRES 28 A 399 GLN ALA ARG SER PHE SER ASP ASP ALA VAL ARG GLY LEU SEQRES 29 A 399 THR ARG TYR HIS TRP PRO GLY ASN VAL ARG GLU LEU MET SEQRES 30 A 399 ASN GLN ILE LYS ARG VAL VAL LEU MET SER ASP THR VAL SEQRES 31 A 399 VAL LEU ASP GLU SER GLN LEU ASP LEU SEQRES 1 D 399 HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO ARG SEQRES 2 D 399 GLY SER HIS MET MET SER THR GLN PHE ARG MET ASP SER SEQRES 3 D 399 VAL PRO GLY SER LEU VAL VAL VAL GLY GLY THR TYR GLU SEQRES 4 D 399 PRO TRP LEU PRO VAL LEU GLU LYS VAL GLY TRP ARG CYS SEQRES 5 D 399 THR GLN VAL ALA ASP LEU ARG LYS PRO ASP ALA LEU PHE SEQRES 6 D 399 VAL GLU THR GLY PRO CYS ILE GLY ILE VAL ASP LEU SER SEQRES 7 D 399 HIS ASP GLU PHE SER LEU ASN GLY ILE ALA ASN LEU VAL SEQRES 8 D 399 SER SER HIS LYS GLN VAL ARG TRP LEU ALA PHE ILE ARG SEQRES 9 D 399 GLU ALA GLN LEU SER SER ASP THR ILE CYS GLN PHE ILE SEQRES 10 D 399 VAL ASN PHE CYS ILE ASP PHE PHE THR ALA PRO ILE PRO SEQRES 11 D 399 ASP ALA GLN LEU LEU SER THR ILE GLY HIS GLN LEU GLY SEQRES 12 D 399 MET LEU LYS LEU GLU LYS LYS VAL TRP PRO HIS PHE GLY SEQRES 13 D 399 SER ALA GLY ASN MET GLY LEU ILE GLY GLU SER MET PRO SEQRES 14 D 399 MET LYS ARG LEU ARG ASP GLN ILE LYS ARG ILE GLY PRO SEQRES 15 D 399 THR ASP VAL SER ILE LEU ILE TYR GLY GLU SER GLY THR SEQRES 16 D 399 GLY LYS GLU THR VAL ALA LYS ALA ILE HIS LYS THR SER SEQRES 17 D 399 SER ARG ALA GLN LYS PRO PHE ILE SER VAL ASN CYS ARG SEQRES 18 D 399 ALA MET SER GLU LYS ARG LEU GLU SER GLU LEU PHE GLY SEQRES 19 D 399 LEU GLY GLU THR GLU GLU GLY GLN GLN PRO PHE LEU LEU SEQRES 20 D 399 GLN ALA ASP GLY GLY THR LEU LEU LEU ASN ASP ILE LEU SEQRES 21 D 399 THR LEU PRO LYS SER GLN GLN LEU ASN LEU LEU ARG PHE SEQRES 22 D 399 LEU GLN GLU GLY THR VAL GLU THR ARG GLN GLY VAL ARG SEQRES 23 D 399 ALA VAL ASP VAL ARG ILE LEU ALA ALA ASN SER SER ASP SEQRES 24 D 399 ILE GLU LYS ALA LEU ILE ASP GLY ASP PHE ASN GLU GLU SEQRES 25 D 399 LEU TYR HIS TYR ILE ASN VAL LEU ARG ILE ASN VAL PRO SEQRES 26 D 399 SER LEU LYS GLU ARG ALA SER ASP ILE VAL LEU LEU ALA SEQRES 27 D 399 LYS HIS PHE LEU GLN GLU TYR SER LYS GLU TYR ASN ALA SEQRES 28 D 399 GLN ALA ARG SER PHE SER ASP ASP ALA VAL ARG GLY LEU SEQRES 29 D 399 THR ARG TYR HIS TRP PRO GLY ASN VAL ARG GLU LEU MET SEQRES 30 D 399 ASN GLN ILE LYS ARG VAL VAL LEU MET SER ASP THR VAL SEQRES 31 D 399 VAL LEU ASP GLU SER GLN LEU ASP LEU HET GTP A 501 32 HET GTP D 501 32 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 3 GTP 2(C10 H16 N5 O14 P3) HELIX 1 AA1 TYR A 21 TRP A 24 5 4 HELIX 2 AA2 LEU A 25 LYS A 30 1 6 HELIX 3 AA3 LEU A 41 GLY A 52 1 12 HELIX 4 AA4 SER A 66 SER A 76 1 11 HELIX 5 AA5 SER A 93 VAL A 101 5 9 HELIX 6 AA6 PRO A 113 TRP A 135 1 23 HELIX 7 AA7 ASN A 143 GLY A 148 5 6 HELIX 8 AA8 MET A 151 GLY A 164 1 14 HELIX 9 AA9 GLY A 179 LYS A 189 1 11 HELIX 10 AB1 SER A 207 SER A 213 1 7 HELIX 11 AB2 PRO A 227 ALA A 232 1 6 HELIX 12 AB3 ASP A 241 LEU A 245 5 5 HELIX 13 AB4 PRO A 246 GLY A 260 1 15 HELIX 14 AB5 ASP A 282 ASP A 289 1 8 HELIX 15 AB6 ASN A 293 ASN A 301 1 9 HELIX 16 AB7 ALA A 314 TYR A 332 1 19 HELIX 17 AB8 SER A 340 THR A 348 1 9 HELIX 18 AB9 GLY A 354 LEU A 368 1 15 HELIX 19 AC1 ASP A 376 LEU A 380 5 5 HELIX 20 AC2 TYR D 21 TRP D 24 5 4 HELIX 21 AC3 LEU D 25 LYS D 30 1 6 HELIX 22 AC4 ARG D 42 GLY D 52 1 11 HELIX 23 AC5 SER D 66 SER D 76 1 11 HELIX 24 AC6 ASP D 94 PHE D 99 1 6 HELIX 25 AC7 ILE D 100 ASN D 102 5 3 HELIX 26 AC8 PRO D 113 HIS D 123 1 11 HELIX 27 AC9 GLN D 124 TRP D 135 1 12 HELIX 28 AD1 PRO D 136 PHE D 138 5 3 HELIX 29 AD2 SER D 140 LEU D 146 5 7 HELIX 30 AD3 MET D 151 GLY D 164 1 14 HELIX 31 AD4 GLY D 179 LYS D 189 1 11 HELIX 32 AD5 ARG D 204 MET D 206 5 3 HELIX 33 AD6 SER D 207 SER D 213 1 7 HELIX 34 AD7 PRO D 227 ALA D 232 1 6 HELIX 35 AD8 PRO D 246 GLY D 260 1 15 HELIX 36 AD9 ASP D 282 ASP D 289 1 8 HELIX 37 AE1 ASN D 293 ASN D 301 1 9 HELIX 38 AE2 SER D 315 LYS D 330 1 16 HELIX 39 AE3 SER D 340 THR D 348 1 9 HELIX 40 AE4 GLY D 354 SER D 370 1 17 HELIX 41 AE5 ASP D 376 LEU D 380 5 5 SHEET 1 AA1 5 ARG A 34 VAL A 38 0 SHEET 2 AA1 5 PRO A 11 VAL A 15 1 N LEU A 14 O THR A 36 SHEET 3 AA1 5 CYS A 54 ASP A 59 1 O ILE A 57 N VAL A 15 SHEET 4 AA1 5 TRP A 82 ARG A 87 1 O ARG A 87 N VAL A 58 SHEET 5 AA1 5 ASP A 106 PHE A 108 1 O PHE A 108 N ILE A 86 SHEET 1 AA2 5 PHE A 198 ASN A 202 0 SHEET 2 AA2 5 THR A 236 ASN A 240 1 O LEU A 238 N ILE A 199 SHEET 3 AA2 5 ARG A 274 ASN A 279 1 O ALA A 278 N LEU A 239 SHEET 4 AA2 5 ILE A 170 GLY A 174 1 N ILE A 172 O ALA A 277 SHEET 5 AA2 5 LEU A 303 VAL A 307 1 O LEU A 303 N LEU A 171 SHEET 1 AA3 2 THR A 261 VAL A 262 0 SHEET 2 AA3 2 ARG A 269 ALA A 270 -1 O ARG A 269 N VAL A 262 SHEET 1 AA4 2 SER A 338 PHE A 339 0 SHEET 2 AA4 2 VAL A 374 LEU A 375 1 O LEU A 375 N SER A 338 SHEET 1 AA5 5 GLN D 37 VAL D 38 0 SHEET 2 AA5 5 GLY D 12 VAL D 15 1 N LEU D 14 O VAL D 38 SHEET 3 AA5 5 ILE D 55 ASP D 59 1 O ILE D 57 N VAL D 15 SHEET 4 AA5 5 ALA D 84 ARG D 87 1 O PHE D 85 N VAL D 58 SHEET 5 AA5 5 PHE D 107 PHE D 108 1 O PHE D 108 N ILE D 86 SHEET 1 AA6 5 PHE D 198 ASN D 202 0 SHEET 2 AA6 5 THR D 236 ASN D 240 1 O LEU D 238 N ILE D 199 SHEET 3 AA6 5 ARG D 274 ASN D 279 1 O ALA D 278 N LEU D 239 SHEET 4 AA6 5 ILE D 170 GLY D 174 1 N ILE D 172 O ALA D 277 SHEET 5 AA6 5 LEU D 303 VAL D 307 1 O LEU D 303 N LEU D 171 SHEET 1 AA7 2 THR D 261 VAL D 262 0 SHEET 2 AA7 2 ARG D 269 ALA D 270 -1 O ARG D 269 N VAL D 262 SHEET 1 AA8 2 SER D 338 PHE D 339 0 SHEET 2 AA8 2 VAL D 374 LEU D 375 1 O LEU D 375 N SER D 338 CISPEP 1 LEU A 215 PHE A 216 0 7.81 CISPEP 2 THR A 221 GLU A 222 0 -19.34 CRYST1 118.639 118.639 78.255 90.00 90.00 120.00 P 31 6 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 0.008429 0.004866 0.000000 0.00000 SCALE2 0.000000 0.009733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012779 0.00000