HEADER TRANSCRIPTION/DNA 21-AUG-12 3VWB TITLE CRYSTAL STRUCTURE OF VIRB CORE DOMAIN (SE-MET DERIVATIVE) COMPLEXED TITLE 2 WITH THE CIS-ACTING SITE (5-BRU MODIFICATIONS) UPSTREAM ICSB PROMOTER COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRULENCE REGULON TRANSCRIPTIONAL ACTIVATOR VIRB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 129-250; COMPND 5 SYNONYM: CELL INVASION REGULATOR INVE; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (26-MER); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (26-MER); COMPND 13 CHAIN: B; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI 2A; SOURCE 3 ORGANISM_TAXID: 42897; SOURCE 4 STRAIN: 301; SOURCE 5 GENE: VIRB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC DNA WITH TWO INTERNAL BR-DU LABELS; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC DNA KEYWDS HTH DNA BINDING MOTIF, DSDNA, PALINDROMIC DNA SEQUENCE, PARB LIKE, KEYWDS 2 HTH DNA-BINDING MOTIF, TRANSCRIPTIONAL ACTIVATOR, SEQUENCE SPECIFIC KEYWDS 3 DSDNA BINDING, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.P.GAO,S.WALTERSPERGER,M.T.WANG,S.CUI REVDAT 5 20-MAR-24 3VWB 1 SEQADV LINK REVDAT 4 25-DEC-13 3VWB 1 JRNL REVDAT 3 11-DEC-13 3VWB 1 JRNL REVDAT 2 04-SEP-13 3VWB 1 JRNL TITLE REVDAT 1 21-AUG-13 3VWB 0 JRNL AUTH X.P.GAO,T.T.ZOU,Z.X.MU,B.QIN,J.YANG,S.WALTERSPERGER, JRNL AUTH 2 M.T.WANG,S.CUI,Q.JIN JRNL TITL STRUCTURAL INSIGHTS INTO VIRB-DNA COMPLEXES REVEAL MECHANISM JRNL TITL 2 OF TRANSCRIPTIONAL ACTIVATION OF VIRULENCE GENES JRNL REF NUCLEIC ACIDS RES. V. 41 10529 2013 JRNL REFN ISSN 0305-1048 JRNL PMID 23985969 JRNL DOI 10.1093/NAR/GKT748 REMARK 2 REMARK 2 RESOLUTION. 2.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 27362 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1358 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 46.8995 - 5.2033 1.00 2611 138 0.1921 0.2240 REMARK 3 2 5.2033 - 4.1308 1.00 2613 131 0.2086 0.2460 REMARK 3 3 4.1308 - 3.6088 1.00 2597 137 0.2245 0.2658 REMARK 3 4 3.6088 - 3.2790 1.00 2594 140 0.2439 0.2875 REMARK 3 5 3.2790 - 3.0440 0.99 2556 134 0.2418 0.2598 REMARK 3 6 3.0440 - 2.8646 1.00 2619 136 0.2704 0.3344 REMARK 3 7 2.8646 - 2.7211 1.00 2638 138 0.2618 0.3229 REMARK 3 8 2.7211 - 2.6027 1.00 2583 136 0.2906 0.2738 REMARK 3 9 2.6027 - 2.5025 1.00 2605 135 0.3179 0.3614 REMARK 3 10 2.5025 - 2.4161 0.98 2588 133 0.3641 0.3900 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL. REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 31.73 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 14.00000 REMARK 3 B22 (A**2) : -7.53350 REMARK 3 B33 (A**2) : -6.46650 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 2144 REMARK 3 ANGLE : 0.979 3103 REMARK 3 CHIRALITY : 0.046 351 REMARK 3 PLANARITY : 0.003 214 REMARK 3 DIHEDRAL : 27.192 868 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 131:132 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.508 62.202 -10.981 REMARK 3 T TENSOR REMARK 3 T11: 0.9949 T22: 1.1345 REMARK 3 T33: 1.0663 T12: -0.0889 REMARK 3 T13: 0.2026 T23: 0.0564 REMARK 3 L TENSOR REMARK 3 L11: 0.0208 L22: 0.0203 REMARK 3 L33: 0.0019 L12: -0.0158 REMARK 3 L13: 0.0054 L23: -0.0074 REMARK 3 S TENSOR REMARK 3 S11: 0.0031 S12: -0.0072 S13: -0.0100 REMARK 3 S21: -0.0148 S22: -0.0218 S23: -0.0101 REMARK 3 S31: -0.0221 S32: 0.0034 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 133:141 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.0691 56.6188 -14.2223 REMARK 3 T TENSOR REMARK 3 T11: 0.1660 T22: 0.4132 REMARK 3 T33: 0.3229 T12: 0.0088 REMARK 3 T13: 0.0347 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.0071 L22: 0.0035 REMARK 3 L33: 0.0040 L12: -0.0015 REMARK 3 L13: -0.0055 L23: 0.0009 REMARK 3 S TENSOR REMARK 3 S11: 0.0578 S12: 0.0346 S13: -0.0589 REMARK 3 S21: -0.0338 S22: -0.0325 S23: -0.0672 REMARK 3 S31: -0.0378 S32: 0.0170 S33: 0.0032 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 142:153 ) REMARK 3 ORIGIN FOR THE GROUP (A): 60.5548 44.2825 -14.1235 REMARK 3 T TENSOR REMARK 3 T11: 0.2086 T22: 0.4770 REMARK 3 T33: 0.2680 T12: 0.0599 REMARK 3 T13: 0.0627 T23: -0.0687 REMARK 3 L TENSOR REMARK 3 L11: 0.0408 L22: 0.0231 REMARK 3 L33: 0.0172 L12: -0.0220 REMARK 3 L13: 0.0048 L23: -0.0158 REMARK 3 S TENSOR REMARK 3 S11: 0.0096 S12: 0.0124 S13: -0.0351 REMARK 3 S21: -0.0301 S22: 0.0374 S23: 0.0698 REMARK 3 S31: 0.0104 S32: 0.1057 S33: 0.0041 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 154:184 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.0637 53.6580 -12.3690 REMARK 3 T TENSOR REMARK 3 T11: 0.2047 T22: 0.4170 REMARK 3 T33: 0.2242 T12: 0.0282 REMARK 3 T13: -0.0380 T23: -0.0640 REMARK 3 L TENSOR REMARK 3 L11: 0.0001 L22: 0.0728 REMARK 3 L33: 0.1286 L12: -0.0128 REMARK 3 L13: -0.0144 L23: -0.0668 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: -0.1433 S13: 0.0241 REMARK 3 S21: -0.1662 S22: -0.0470 S23: -0.1001 REMARK 3 S31: -0.1149 S32: 0.1516 S33: -0.0888 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 185:208 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.8389 52.5316 -15.2894 REMARK 3 T TENSOR REMARK 3 T11: 0.2568 T22: 0.5047 REMARK 3 T33: 0.2981 T12: -0.0272 REMARK 3 T13: -0.0030 T23: -0.0683 REMARK 3 L TENSOR REMARK 3 L11: 0.0201 L22: 0.0040 REMARK 3 L33: 0.0114 L12: -0.0051 REMARK 3 L13: -0.0090 L23: 0.0167 REMARK 3 S TENSOR REMARK 3 S11: 0.0358 S12: -0.1683 S13: -0.0489 REMARK 3 S21: 0.2067 S22: -0.0601 S23: -0.0151 REMARK 3 S31: -0.0605 S32: -0.0244 S33: -0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 209:224 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.4508 59.8400 -24.8152 REMARK 3 T TENSOR REMARK 3 T11: 0.1713 T22: 0.5272 REMARK 3 T33: 0.1125 T12: 0.1384 REMARK 3 T13: -0.2243 T23: -0.1158 REMARK 3 L TENSOR REMARK 3 L11: 0.0127 L22: 0.0153 REMARK 3 L33: 0.0073 L12: 0.0142 REMARK 3 L13: 0.0066 L23: 0.0045 REMARK 3 S TENSOR REMARK 3 S11: -0.0181 S12: 0.1072 S13: -0.0577 REMARK 3 S21: -0.0947 S22: 0.0031 S23: -0.0136 REMARK 3 S31: 0.0074 S32: 0.0204 S33: -0.1083 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 225:234 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.9166 71.4215 -12.5223 REMARK 3 T TENSOR REMARK 3 T11: 0.4604 T22: 0.4830 REMARK 3 T33: 0.6408 T12: 0.1760 REMARK 3 T13: 0.1514 T23: -0.1762 REMARK 3 L TENSOR REMARK 3 L11: 0.0020 L22: 0.0034 REMARK 3 L33: 0.0094 L12: -0.0014 REMARK 3 L13: -0.0020 L23: -0.0041 REMARK 3 S TENSOR REMARK 3 S11: 0.0099 S12: -0.0034 S13: 0.0781 REMARK 3 S21: -0.0283 S22: 0.0329 S23: 0.0387 REMARK 3 S31: -0.0478 S32: -0.0093 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 235:241 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.9323 60.6065 -13.2379 REMARK 3 T TENSOR REMARK 3 T11: 0.2926 T22: 0.7664 REMARK 3 T33: 0.2828 T12: 0.1809 REMARK 3 T13: -0.0486 T23: -0.1456 REMARK 3 L TENSOR REMARK 3 L11: 0.0064 L22: 0.0528 REMARK 3 L33: 0.0406 L12: -0.0167 REMARK 3 L13: 0.0071 L23: 0.0073 REMARK 3 S TENSOR REMARK 3 S11: -0.0605 S12: -0.0046 S13: 0.0246 REMARK 3 S21: -0.0124 S22: -0.0192 S23: 0.0132 REMARK 3 S31: 0.0630 S32: -0.0585 S33: -0.0157 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN A AND RESID 242:246 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.3464 52.0149 -15.6255 REMARK 3 T TENSOR REMARK 3 T11: 0.8272 T22: 0.6671 REMARK 3 T33: 0.5633 T12: 0.0879 REMARK 3 T13: 0.2322 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.0025 L22: 0.0043 REMARK 3 L33: 0.0006 L12: 0.0003 REMARK 3 L13: -0.0014 L23: -0.0001 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: 0.0105 S13: -0.0195 REMARK 3 S21: 0.0396 S22: -0.0115 S23: 0.0304 REMARK 3 S31: -0.0104 S32: -0.0176 S33: -0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:4 ) REMARK 3 ORIGIN FOR THE GROUP (A): 41.7223 20.0122 -4.7936 REMARK 3 T TENSOR REMARK 3 T11: 1.2728 T22: 0.5870 REMARK 3 T33: 1.3996 T12: -0.1677 REMARK 3 T13: 0.1989 T23: -0.0496 REMARK 3 L TENSOR REMARK 3 L11: 0.0041 L22: 0.0096 REMARK 3 L33: 0.0003 L12: -0.0034 REMARK 3 L13: -0.0011 L23: 0.0038 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: -0.0817 S13: -0.0320 REMARK 3 S21: 0.0137 S22: -0.0032 S23: 0.0613 REMARK 3 S31: -0.0371 S32: -0.0819 S33: -0.0001 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: ( CHAIN B AND RESID 5:13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.8948 38.8347 -1.5178 REMARK 3 T TENSOR REMARK 3 T11: 0.3066 T22: 0.2419 REMARK 3 T33: 0.3396 T12: -0.0156 REMARK 3 T13: 0.0365 T23: -0.0984 REMARK 3 L TENSOR REMARK 3 L11: 0.0782 L22: 0.0149 REMARK 3 L33: 0.0564 L12: -0.0255 REMARK 3 L13: 0.0232 L23: -0.0383 REMARK 3 S TENSOR REMARK 3 S11: -0.1463 S12: -0.0090 S13: -0.2736 REMARK 3 S21: 0.2188 S22: -0.0625 S23: -0.0374 REMARK 3 S31: 0.3103 S32: -0.1224 S33: -0.0312 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: ( CHAIN B AND RESID 14:26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 45.0622 74.5048 8.0250 REMARK 3 T TENSOR REMARK 3 T11: 1.2613 T22: -0.2726 REMARK 3 T33: 0.6308 T12: 0.0463 REMARK 3 T13: -0.0458 T23: -0.1980 REMARK 3 L TENSOR REMARK 3 L11: 0.2919 L22: 0.0815 REMARK 3 L33: 0.1146 L12: 0.1192 REMARK 3 L13: -0.0906 L23: -0.0966 REMARK 3 S TENSOR REMARK 3 S11: 0.0167 S12: -0.3659 S13: 0.6782 REMARK 3 S21: 0.2129 S22: -0.4215 S23: 0.2711 REMARK 3 S31: -0.8303 S32: -0.1494 S33: -0.2904 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: ( CHAIN C AND RESID 1:13 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.8111 83.9020 7.2545 REMARK 3 T TENSOR REMARK 3 T11: 1.4456 T22: -0.2647 REMARK 3 T33: 0.8542 T12: 0.3357 REMARK 3 T13: 0.0559 T23: -0.2449 REMARK 3 L TENSOR REMARK 3 L11: 0.0085 L22: 0.2360 REMARK 3 L33: 0.1757 L12: 0.0455 REMARK 3 L13: -0.0250 L23: 0.0654 REMARK 3 S TENSOR REMARK 3 S11: -0.1527 S12: 0.0261 S13: 0.5861 REMARK 3 S21: 0.2017 S22: -0.1798 S23: -0.1416 REMARK 3 S31: -0.2510 S32: -0.1849 S33: -0.3909 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: ( CHAIN C AND RESID 14:26 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.2398 43.7899 -0.8431 REMARK 3 T TENSOR REMARK 3 T11: 0.5248 T22: 0.2195 REMARK 3 T33: 0.3159 T12: 0.0090 REMARK 3 T13: 0.0967 T23: -0.0434 REMARK 3 L TENSOR REMARK 3 L11: 0.0830 L22: 0.0293 REMARK 3 L33: 0.0952 L12: 0.0586 REMARK 3 L13: -0.0393 L23: -0.0526 REMARK 3 S TENSOR REMARK 3 S11: -0.1098 S12: -0.0144 S13: -0.2025 REMARK 3 S21: -0.0032 S22: -0.1237 S23: -0.0308 REMARK 3 S31: 0.2887 S32: 0.0825 S33: -0.0218 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. REMARK 4 REMARK 4 3VWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000095580. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR CRYSTAL REMARK 200 TYPE SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS PACKAGE REMARK 200 DATA SCALING SOFTWARE : XDS PACKAGE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27467 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.416 REMARK 200 RESOLUTION RANGE LOW (A) : 46.891 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.770 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.5600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.54 REMARK 200 R MERGE FOR SHELL (I) : 0.76800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.430 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MGCL2, 0.1M SODIUM ACETATE, 22% REMARK 280 PEG400, 3%(V/V) DIMETHYL SULFOXIDE, PH 4.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 28.66050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 81.52550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.66050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 81.52550 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 108 REMARK 465 GLY A 109 REMARK 465 SER A 110 REMARK 465 SER A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 SER A 118 REMARK 465 SER A 119 REMARK 465 GLY A 120 REMARK 465 LEU A 121 REMARK 465 VAL A 122 REMARK 465 PRO A 123 REMARK 465 ARG A 124 REMARK 465 GLY A 125 REMARK 465 SER A 126 REMARK 465 HIS A 127 REMARK 465 MET A 128 REMARK 465 ALA A 129 REMARK 465 LYS A 130 REMARK 465 ARG A 247 REMARK 465 LYS A 248 REMARK 465 GLN A 249 REMARK 465 ASN A 250 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 H2'' BRU C 21 O5' DC C 22 1.59 REMARK 500 O LYS A 218 O HOH A 318 1.97 REMARK 500 O HOH B 111 O HOH B 113 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 DT C 9 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 24 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 2 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT B 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG B 7 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG B 19 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 26 O4' - C1' - N9 ANGL. DEV. = 3.8 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 233 -96.80 74.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NTZ RELATED DB: PDB REMARK 900 RELATED ID: 1ZX4 RELATED DB: PDB REMARK 900 RELATED ID: 3MKZ RELATED DB: PDB DBREF 3VWB A 129 250 UNP P0A247 VIRB_SHIFL 129 250 DBREF 3VWB C 1 26 PDB 3VWB 3VWB 1 26 DBREF 3VWB B 1 26 PDB 3VWB 3VWB 1 26 SEQADV 3VWB MET A 108 UNP P0A247 EXPRESSION TAG SEQADV 3VWB GLY A 109 UNP P0A247 EXPRESSION TAG SEQADV 3VWB SER A 110 UNP P0A247 EXPRESSION TAG SEQADV 3VWB SER A 111 UNP P0A247 EXPRESSION TAG SEQADV 3VWB HIS A 112 UNP P0A247 EXPRESSION TAG SEQADV 3VWB HIS A 113 UNP P0A247 EXPRESSION TAG SEQADV 3VWB HIS A 114 UNP P0A247 EXPRESSION TAG SEQADV 3VWB HIS A 115 UNP P0A247 EXPRESSION TAG SEQADV 3VWB HIS A 116 UNP P0A247 EXPRESSION TAG SEQADV 3VWB HIS A 117 UNP P0A247 EXPRESSION TAG SEQADV 3VWB SER A 118 UNP P0A247 EXPRESSION TAG SEQADV 3VWB SER A 119 UNP P0A247 EXPRESSION TAG SEQADV 3VWB GLY A 120 UNP P0A247 EXPRESSION TAG SEQADV 3VWB LEU A 121 UNP P0A247 EXPRESSION TAG SEQADV 3VWB VAL A 122 UNP P0A247 EXPRESSION TAG SEQADV 3VWB PRO A 123 UNP P0A247 EXPRESSION TAG SEQADV 3VWB ARG A 124 UNP P0A247 EXPRESSION TAG SEQADV 3VWB GLY A 125 UNP P0A247 EXPRESSION TAG SEQADV 3VWB SER A 126 UNP P0A247 EXPRESSION TAG SEQADV 3VWB HIS A 127 UNP P0A247 EXPRESSION TAG SEQADV 3VWB MET A 128 UNP P0A247 EXPRESSION TAG SEQRES 1 A 143 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 143 LEU VAL PRO ARG GLY SER HIS MET ALA LYS GLU HIS SER SEQRES 3 A 143 ILE ARG GLU LEU GLY ILE GLY LEU ASN PHE LEU LYS VAL SEQRES 4 A 143 SER GLY MET SER TYR LYS ASP ILE ALA LYS LYS GLU ASN SEQRES 5 A 143 LEU SER ARG ALA LYS VAL THR ARG ALA PHE GLN ALA ALA SEQRES 6 A 143 SER VAL PRO GLN GLU ILE ILE SER LEU PHE PRO ILE ALA SEQRES 7 A 143 SER GLU LEU ASN PHE ASN ASP TYR LYS ILE LEU PHE ASN SEQRES 8 A 143 TYR TYR LYS GLY LEU GLU LYS ALA ASN GLU SER LEU SER SEQRES 9 A 143 SER THR LEU PRO ILE LEU LYS GLU GLU ILE LYS ASP LEU SEQRES 10 A 143 ASP THR ASN LEU PRO PRO ASP ILE TYR LYS LYS GLU ILE SEQRES 11 A 143 LEU ASN ILE ILE LYS LYS SER LYS ASN ARG LYS GLN ASN SEQRES 1 C 26 DA DA DA DC BRU DC DG DT DT DT DC DA DT SEQRES 2 C 26 DC DA DT DG DA DA DA BRU DC DC DC DA DC SEQRES 1 B 26 DT DT DT DG DT DG DG DG DA DT DT DT DC SEQRES 2 B 26 DA DT DG DA DT DG DA DA DA DC DG DA DG MODRES 3VWB BRU C 5 DU MODRES 3VWB BRU C 21 DU HET BRU C 5 29 HET BRU C 21 29 HETNAM BRU 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE FORMUL 2 BRU 2(C9 H12 BR N2 O8 P) FORMUL 4 HOH *62(H2 O) HELIX 1 1 SER A 133 LEU A 141 1 9 HELIX 2 2 LEU A 141 VAL A 146 1 6 HELIX 3 3 SER A 150 ASN A 159 1 10 HELIX 4 4 SER A 161 SER A 173 1 13 HELIX 5 5 PRO A 175 LEU A 181 1 7 HELIX 6 6 ILE A 184 LEU A 188 5 5 HELIX 7 7 ASN A 189 ALA A 206 1 18 HELIX 8 8 THR A 213 ASP A 223 1 11 HELIX 9 9 TYR A 233 ASN A 246 1 14 LINK O3' DC C 4 P BRU C 5 1555 1555 1.63 LINK O3' BRU C 5 P DC C 6 1555 1555 1.63 LINK O3' DA C 20 P BRU C 21 1555 1555 1.60 LINK O3' BRU C 21 P DC C 22 1555 1555 1.61 CISPEP 1 THR A 226 ASN A 227 0 0.65 CISPEP 2 ILE A 232 TYR A 233 0 -0.25 CRYST1 57.321 163.051 39.569 90.00 90.00 90.00 P 21 21 2 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 0.017446 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006133 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025272 0.00000