HEADER TRANSCRIPTION/DNA 19-DEC-12 3W3C TITLE CRYSTAL STRUCTURE OF VIRB CORE DOMAIN COMPLEXED WITH THE CIS-ACTING TITLE 2 SITE 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: B; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (26-MER); COMPND 13 CHAIN: C; 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: ROSETTA 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; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC DNA KEYWDS HTH DNA BINDING MOTIF, PROTEIN-DNA COMPLEX, PARB BOX-A LIKE SEQUENCE, KEYWDS 2 PARB LIKE FOLD, TRANSCRIPTIONAL ACTIVATOR, SEQUENCE SPECIFIC DSDNA KEYWDS 3 BINDING, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.P.GAO,S.WALTERSPERGER,M.T.WANG,S.CUI REVDAT 4 08-NOV-23 3W3C 1 SEQADV REVDAT 3 25-DEC-13 3W3C 1 JRNL REVDAT 2 11-DEC-13 3W3C 1 JRNL REVDAT 1 04-SEP-13 3W3C 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. 2.43 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) : 2.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.880 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 13893 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.265 REMARK 3 R VALUE (WORKING SET) : 0.264 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 694 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 40.8557 - 4.1564 0.99 2868 151 0.2058 0.2245 REMARK 3 2 4.1564 - 3.2995 0.87 2367 125 0.2843 0.2935 REMARK 3 3 3.2995 - 2.8826 0.99 2695 140 0.2910 0.2874 REMARK 3 4 2.8826 - 2.6191 1.00 2686 142 0.3181 0.3579 REMARK 3 5 2.6191 - 2.4314 0.97 2583 136 0.3532 0.3778 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 : 0.33 REMARK 3 B_SOL : 30.72 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.09650 REMARK 3 B22 (A**2) : -7.11430 REMARK 3 B33 (A**2) : -3.98220 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 : 0.002 2134 REMARK 3 ANGLE : 0.748 3101 REMARK 3 CHIRALITY : 0.036 351 REMARK 3 PLANARITY : 0.003 212 REMARK 3 DIHEDRAL : 25.488 882 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 131:156) REMARK 3 ORIGIN FOR THE GROUP (A): -30.1676 -30.8138 32.8952 REMARK 3 T TENSOR REMARK 3 T11: 0.2134 T22: 0.4341 REMARK 3 T33: 0.2570 T12: -0.0070 REMARK 3 T13: 0.0321 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 0.0452 L22: 0.0187 REMARK 3 L33: 0.1317 L12: -0.0086 REMARK 3 L13: 0.0505 L23: -0.0427 REMARK 3 S TENSOR REMARK 3 S11: -0.0433 S12: -0.2066 S13: -0.0088 REMARK 3 S21: 0.0741 S22: -0.0225 S23: 0.0760 REMARK 3 S31: -0.1410 S32: -0.1382 S33: -0.0045 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 157:193) REMARK 3 ORIGIN FOR THE GROUP (A): -20.5265 -25.2779 31.9355 REMARK 3 T TENSOR REMARK 3 T11: 0.1886 T22: 0.3965 REMARK 3 T33: 0.1426 T12: -0.0668 REMARK 3 T13: -0.0444 T23: 0.0892 REMARK 3 L TENSOR REMARK 3 L11: 0.0767 L22: 0.2150 REMARK 3 L33: 0.1508 L12: -0.0320 REMARK 3 L13: 0.0279 L23: -0.0283 REMARK 3 S TENSOR REMARK 3 S11: 0.0489 S12: 0.2339 S13: 0.0360 REMARK 3 S21: 0.0940 S22: -0.1034 S23: 0.0714 REMARK 3 S31: -0.2245 S32: 0.0617 S33: -0.1212 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 194:242) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3790 -23.1483 38.2605 REMARK 3 T TENSOR REMARK 3 T11: 0.2558 T22: 0.4915 REMARK 3 T33: 0.2456 T12: -0.0903 REMARK 3 T13: -0.1154 T23: 0.0951 REMARK 3 L TENSOR REMARK 3 L11: 0.3417 L22: 0.0424 REMARK 3 L33: 0.1070 L12: -0.1092 REMARK 3 L13: -0.1646 L23: 0.0678 REMARK 3 S TENSOR REMARK 3 S11: -0.1812 S12: 0.0068 S13: -0.0742 REMARK 3 S21: -0.0031 S22: 0.0561 S23: -0.0994 REMARK 3 S31: -0.0309 S32: 0.1742 S33: -0.2113 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 243:246) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2424 -29.7580 36.7095 REMARK 3 T TENSOR REMARK 3 T11: 1.2574 T22: 1.0956 REMARK 3 T33: 1.4618 T12: -0.1141 REMARK 3 T13: 0.1041 T23: -0.0338 REMARK 3 L TENSOR REMARK 3 L11: 0.0055 L22: 0.0680 REMARK 3 L33: 0.0156 L12: 0.0202 REMARK 3 L13: 0.0100 L23: 0.0327 REMARK 3 S TENSOR REMARK 3 S11: -0.0052 S12: 0.0018 S13: -0.0056 REMARK 3 S21: 0.0102 S22: 0.0043 S23: 0.0006 REMARK 3 S31: 0.0075 S32: 0.0101 S33: 0.0004 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN B AND RESID 1:19) REMARK 3 ORIGIN FOR THE GROUP (A): -19.1836 -38.2599 19.3835 REMARK 3 T TENSOR REMARK 3 T11: 0.3141 T22: 0.1477 REMARK 3 T33: 0.3095 T12: 0.0009 REMARK 3 T13: 0.0852 T23: 0.0356 REMARK 3 L TENSOR REMARK 3 L11: 0.1288 L22: 0.0794 REMARK 3 L33: 0.2878 L12: 0.0779 REMARK 3 L13: 0.1278 L23: 0.1425 REMARK 3 S TENSOR REMARK 3 S11: -0.0574 S12: -0.0632 S13: -0.0399 REMARK 3 S21: -0.1581 S22: -0.1709 S23: -0.0479 REMARK 3 S31: 0.0744 S32: 0.0254 S33: -0.2007 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN B AND RESID 20:26) REMARK 3 ORIGIN FOR THE GROUP (A): -12.1932 3.0182 10.7374 REMARK 3 T TENSOR REMARK 3 T11: 1.4484 T22: 0.4092 REMARK 3 T33: 1.1304 T12: -0.0338 REMARK 3 T13: 0.0005 T23: 0.1731 REMARK 3 L TENSOR REMARK 3 L11: 0.0597 L22: 0.0127 REMARK 3 L33: 0.0405 L12: 0.0149 REMARK 3 L13: -0.0141 L23: -0.0173 REMARK 3 S TENSOR REMARK 3 S11: 0.1139 S12: -0.1299 S13: 0.1323 REMARK 3 S21: -0.0498 S22: -0.1189 S23: -0.0609 REMARK 3 S31: -0.0508 S32: 0.0958 S33: 0.0038 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN C AND RESID 1:12) REMARK 3 ORIGIN FOR THE GROUP (A): -13.9341 4.0738 11.9461 REMARK 3 T TENSOR REMARK 3 T11: 0.9445 T22: -0.1818 REMARK 3 T33: 1.1210 T12: -0.5108 REMARK 3 T13: 0.0525 T23: 0.2574 REMARK 3 L TENSOR REMARK 3 L11: 0.0207 L22: 0.0710 REMARK 3 L33: 0.2715 L12: -0.0280 REMARK 3 L13: -0.0577 L23: 0.0396 REMARK 3 S TENSOR REMARK 3 S11: 0.0353 S12: 0.0062 S13: 0.0672 REMARK 3 S21: -0.0717 S22: -0.0607 S23: 0.0491 REMARK 3 S31: 0.0317 S32: 0.1147 S33: 0.0726 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN C AND RESID 13:26) REMARK 3 ORIGIN FOR THE GROUP (A): -19.8440 -35.8061 20.5745 REMARK 3 T TENSOR REMARK 3 T11: 0.3682 T22: 0.2461 REMARK 3 T33: 0.3462 T12: -0.0059 REMARK 3 T13: 0.0471 T23: 0.0428 REMARK 3 L TENSOR REMARK 3 L11: 0.0639 L22: 0.0469 REMARK 3 L33: 0.1432 L12: -0.0678 REMARK 3 L13: -0.1058 L23: 0.0882 REMARK 3 S TENSOR REMARK 3 S11: 0.0401 S12: 0.0366 S13: -0.1453 REMARK 3 S21: -0.2049 S22: -0.1618 S23: 0.1048 REMARK 3 S31: 0.0236 S32: 0.1785 S33: 0.0000 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 3W3C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000095833. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.3 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) : 1.54001 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS PACKAGE REMARK 200 DATA SCALING SOFTWARE : XDS PACKAGE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13895 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.430 REMARK 200 RESOLUTION RANGE LOW (A) : 40.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 4.950 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.04900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.97 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.770 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER FOR MR REMARK 200 STARTING MODEL: PDB ENTRY: 3VWB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MGCL2, 0.1M SODIUM ACETATE, 30% REMARK 280 PEG400, 8%(V/V)1,3-BUTANEDIOL, PH 4.3, VAPOR DIFFUSION, REMARK 280 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 28.07000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 81.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.07000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 81.70000 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: 3490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 HIS A 132 CB CG ND1 CD2 CE1 NE2 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 HZ3 LYS A 194 O HOH A 327 1.56 REMARK 500 O HOH A 302 O HOH A 326 1.85 REMARK 500 O HOH A 324 O HOH B 103 1.89 REMARK 500 O HOH A 307 O HOH B 105 2.03 REMARK 500 OG SER A 244 O HOH A 304 2.04 REMARK 500 OH TYR A 193 O HOH A 325 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 153 O HOH A 320 4447 1.96 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 DG B 19 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 2 C3' - C2' - C1' ANGL. DEV. = -6.5 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 2.5 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 ASP A 225 105.80 -55.21 REMARK 500 PRO A 230 -77.15 -94.83 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 REMARK 900 RELATED ID: 3VWB RELATED DB: PDB REMARK 900 RELATED ID: 3W2A RELATED DB: PDB DBREF 3W3C A 129 250 UNP P0A247 VIRB_SHIFL 129 250 DBREF 3W3C B 1 26 PDB 3W3C 3W3C 1 26 DBREF 3W3C C 1 26 PDB 3W3C 3W3C 1 26 SEQADV 3W3C MET A 108 UNP P0A247 EXPRESSION TAG SEQADV 3W3C GLY A 109 UNP P0A247 EXPRESSION TAG SEQADV 3W3C SER A 110 UNP P0A247 EXPRESSION TAG SEQADV 3W3C SER A 111 UNP P0A247 EXPRESSION TAG SEQADV 3W3C HIS A 112 UNP P0A247 EXPRESSION TAG SEQADV 3W3C HIS A 113 UNP P0A247 EXPRESSION TAG SEQADV 3W3C HIS A 114 UNP P0A247 EXPRESSION TAG SEQADV 3W3C HIS A 115 UNP P0A247 EXPRESSION TAG SEQADV 3W3C HIS A 116 UNP P0A247 EXPRESSION TAG SEQADV 3W3C HIS A 117 UNP P0A247 EXPRESSION TAG SEQADV 3W3C SER A 118 UNP P0A247 EXPRESSION TAG SEQADV 3W3C SER A 119 UNP P0A247 EXPRESSION TAG SEQADV 3W3C GLY A 120 UNP P0A247 EXPRESSION TAG SEQADV 3W3C LEU A 121 UNP P0A247 EXPRESSION TAG SEQADV 3W3C VAL A 122 UNP P0A247 EXPRESSION TAG SEQADV 3W3C PRO A 123 UNP P0A247 EXPRESSION TAG SEQADV 3W3C ARG A 124 UNP P0A247 EXPRESSION TAG SEQADV 3W3C GLY A 125 UNP P0A247 EXPRESSION TAG SEQADV 3W3C SER A 126 UNP P0A247 EXPRESSION TAG SEQADV 3W3C HIS A 127 UNP P0A247 EXPRESSION TAG SEQADV 3W3C 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 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 SEQRES 1 C 26 DA DA DA DC DT DC DG DT DT DT DC DA DT SEQRES 2 C 26 DC DA DT DG DA DA DA DT DC DC DC DA DC FORMUL 4 HOH *70(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 GLU A 158 1 9 HELIX 4 4 SER A 161 SER A 173 1 13 HELIX 5 5 PRO A 175 SER A 180 1 6 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 LEU A 224 1 12 HELIX 9 9 ASP A 231 ASN A 246 1 16 CISPEP 1 THR A 226 ASN A 227 0 1.64 CRYST1 56.140 163.400 39.670 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 0.017813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025208 0.00000