HEADER VIRAL PROTEIN 24-OCT-11 3VJJ TITLE CRYSTAL STRUCTURE ANALYSIS OF THE P9-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: P9-1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RICE BLACK STREAKED DWARF VIRUS; SOURCE 3 ORGANISM_COMMON: RBSDV; SOURCE 4 ORGANISM_TAXID: 10990; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIROPLASM, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.AKITA,A.HIGASHIURA,M.SUZUKI,T.TSUKIHARA,A.NAKAGAWA,T.OMURA REVDAT 3 20-MAR-24 3VJJ 1 SEQADV REVDAT 2 17-JUL-13 3VJJ 1 JRNL REVDAT 1 21-DEC-11 3VJJ 0 JRNL AUTH F.AKITA,A.HIGASHIURA,T.SHIMIZU,Y.PU,M.SUZUKI, JRNL AUTH 2 T.UEHARA-ICHIKI,T.SASAYA,S.KANAMARU,F.ARISAKA,T.TSUKIHARA, JRNL AUTH 3 A.NAKAGAWA,T.OMURA JRNL TITL CRYSTALLOGRAPHIC ANALYSIS REVEALS OCTAMERIZATION OF JRNL TITL 2 VIROPLASM MATRIX PROTEIN P9-1 OF RICE BLACK STREAKED DWARF JRNL TITL 3 VIRUS JRNL REF J.VIROL. V. 86 746 2012 JRNL REFN ISSN 0022-538X JRNL PMID 22072761 JRNL DOI 10.1128/JVI.00826-11 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 22911 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.250 REMARK 3 FREE R VALUE TEST SET COUNT : 974 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 42.1801 - 5.7349 0.96 3355 166 0.2726 0.3247 REMARK 3 2 5.7349 - 4.5537 1.00 3302 171 0.2021 0.2629 REMARK 3 3 4.5537 - 3.9786 0.99 3222 177 0.1919 0.2429 REMARK 3 4 3.9786 - 3.6150 0.98 3225 131 0.2362 0.3164 REMARK 3 5 3.6150 - 3.3560 0.96 3122 142 0.2696 0.3091 REMARK 3 6 3.3560 - 3.1582 0.91 3008 96 0.3050 0.2853 REMARK 3 7 3.1582 - 3.0001 0.82 2703 91 0.3472 0.4011 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.50 REMARK 3 SHRINKAGE RADIUS : 0.16 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 102.7 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 92.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 116.2 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 14.08800 REMARK 3 B22 (A**2) : 14.08800 REMARK 3 B33 (A**2) : -28.17610 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 : 0.013 4553 REMARK 3 ANGLE : 1.654 6127 REMARK 3 CHIRALITY : 0.111 695 REMARK 3 PLANARITY : 0.009 775 REMARK 3 DIHEDRAL : 20.034 1743 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 15.8625 -33.7116 -34.0010 REMARK 3 T TENSOR REMARK 3 T11: 0.2670 T22: 0.3451 REMARK 3 T33: 0.3222 T12: -0.0393 REMARK 3 T13: 0.0014 T23: -0.0215 REMARK 3 L TENSOR REMARK 3 L11: 0.7361 L22: 0.8289 REMARK 3 L33: 0.7641 L12: 0.2993 REMARK 3 L13: -0.0850 L23: -0.1990 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: 0.3219 S13: 0.0455 REMARK 3 S21: -0.1497 S22: 0.1909 S23: 0.0282 REMARK 3 S31: 0.0990 S32: -0.2109 S33: -0.0771 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A AND (RESSEQ 26:41 OR RESSEQ REMARK 3 63:126 OR RESSEQ 164:194 OR RESSEQ 202: REMARK 3 262 OR RESSEQ 265:313 OR RESSEQ 324:346 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 26:41 OR RESSEQ REMARK 3 63:126 OR RESSEQ 164:194 OR RESSEQ 202: REMARK 3 262 OR RESSEQ 265:313 OR RESSEQ 324:346 ) REMARK 3 ATOM PAIRS NUMBER : 2006 REMARK 3 RMSD : 0.073 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3VJJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000095123. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-10; 11-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; PHOTON FACTORY REMARK 200 BEAMLINE : BL44XU; AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9; 0.97907, 0.97931, 0.96408 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24512 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 44.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 63.64200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 63.64200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 63.64200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 63.64200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 63.64200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.64200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 63.64200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.64200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 25840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 107370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -155.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -127.28400 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 -63.64200 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 -63.64200 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 63.64200 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 -63.64200 REMARK 350 BIOMT3 4 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 SER A 2 REMARK 465 TYR A 3 REMARK 465 TYR A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 LEU A 11 REMARK 465 GLY A 12 REMARK 465 SER A 13 REMARK 465 THR A 14 REMARK 465 SER A 15 REMARK 465 LEU A 16 REMARK 465 TYR A 17 REMARK 465 LYS A 18 REMARK 465 LYS A 19 REMARK 465 ALA A 20 REMARK 465 GLY A 21 REMARK 465 MET A 22 REMARK 465 ALA A 23 REMARK 465 ASP A 24 REMARK 465 ASN A 42 REMARK 465 ASP A 43 REMARK 465 GLN A 44 REMARK 465 PRO A 45 REMARK 465 ASN A 46 REMARK 465 ARG A 47 REMARK 465 ASN A 48 REMARK 465 THR A 49 REMARK 465 ASN A 50 REMARK 465 SER A 51 REMARK 465 SER A 52 REMARK 465 THR A 53 REMARK 465 SER A 54 REMARK 465 GLN A 55 REMARK 465 SER A 56 REMARK 465 THR A 57 REMARK 465 GLU A 58 REMARK 465 ASN A 59 REMARK 465 ARG A 60 REMARK 465 LEU A 61 REMARK 465 SER A 62 REMARK 465 TYR A 129 REMARK 465 ASP A 130 REMARK 465 ARG A 131 REMARK 465 GLN A 132 REMARK 465 ALA A 133 REMARK 465 ASN A 134 REMARK 465 ILE A 135 REMARK 465 SER A 136 REMARK 465 VAL A 137 REMARK 465 LYS A 138 REMARK 465 SER A 139 REMARK 465 PRO A 140 REMARK 465 ASP A 141 REMARK 465 PHE A 142 REMARK 465 THR A 143 REMARK 465 LEU A 144 REMARK 465 LEU A 145 REMARK 465 LEU A 146 REMARK 465 GLU A 147 REMARK 465 TYR A 148 REMARK 465 THR A 149 REMARK 465 LEU A 150 REMARK 465 LYS A 151 REMARK 465 PRO A 152 REMARK 465 SER A 153 REMARK 465 SER A 154 REMARK 465 GLU A 155 REMARK 465 THR A 156 REMARK 465 ASP A 157 REMARK 465 PRO A 158 REMARK 465 THR A 159 REMARK 465 ILE A 160 REMARK 465 PRO A 161 REMARK 465 GLU A 162 REMARK 465 ASN A 163 REMARK 465 SER A 314 REMARK 465 ASN A 315 REMARK 465 THR A 316 REMARK 465 LEU A 317 REMARK 465 ARG A 318 REMARK 465 GLY A 319 REMARK 465 ALA A 320 REMARK 465 SER A 321 REMARK 465 ARG A 322 REMARK 465 GLN A 323 REMARK 465 VAL A 368 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 TYR B 3 REMARK 465 TYR B 4 REMARK 465 HIS B 5 REMARK 465 HIS B 6 REMARK 465 HIS B 7 REMARK 465 HIS B 8 REMARK 465 HIS B 9 REMARK 465 HIS B 10 REMARK 465 LEU B 11 REMARK 465 GLY B 12 REMARK 465 SER B 13 REMARK 465 THR B 14 REMARK 465 SER B 15 REMARK 465 LEU B 16 REMARK 465 TYR B 17 REMARK 465 LYS B 18 REMARK 465 LYS B 19 REMARK 465 ALA B 20 REMARK 465 GLY B 21 REMARK 465 MET B 22 REMARK 465 ALA B 23 REMARK 465 ASP B 24 REMARK 465 GLN B 25 REMARK 465 ASP B 43 REMARK 465 GLN B 44 REMARK 465 PRO B 45 REMARK 465 ASN B 46 REMARK 465 ARG B 47 REMARK 465 ASN B 48 REMARK 465 THR B 49 REMARK 465 ASN B 50 REMARK 465 SER B 51 REMARK 465 SER B 52 REMARK 465 THR B 53 REMARK 465 SER B 54 REMARK 465 GLN B 55 REMARK 465 SER B 56 REMARK 465 THR B 57 REMARK 465 GLU B 58 REMARK 465 ASN B 59 REMARK 465 ARG B 60 REMARK 465 LEU B 61 REMARK 465 SER B 62 REMARK 465 TYR B 129 REMARK 465 ASP B 130 REMARK 465 ARG B 131 REMARK 465 GLN B 132 REMARK 465 ALA B 133 REMARK 465 ASN B 134 REMARK 465 ILE B 135 REMARK 465 SER B 136 REMARK 465 VAL B 137 REMARK 465 LYS B 138 REMARK 465 SER B 139 REMARK 465 PRO B 140 REMARK 465 ASP B 141 REMARK 465 PHE B 142 REMARK 465 THR B 143 REMARK 465 LEU B 144 REMARK 465 LEU B 145 REMARK 465 LEU B 146 REMARK 465 GLU B 147 REMARK 465 TYR B 148 REMARK 465 THR B 149 REMARK 465 LEU B 150 REMARK 465 LYS B 151 REMARK 465 PRO B 152 REMARK 465 SER B 153 REMARK 465 SER B 154 REMARK 465 GLU B 155 REMARK 465 THR B 156 REMARK 465 ASP B 157 REMARK 465 PRO B 158 REMARK 465 THR B 159 REMARK 465 ILE B 160 REMARK 465 PRO B 161 REMARK 465 GLU B 162 REMARK 465 ASN B 163 REMARK 465 GLU B 197 REMARK 465 SER B 198 REMARK 465 GLU B 199 REMARK 465 GLU B 200 REMARK 465 SER B 201 REMARK 465 PRO B 263 REMARK 465 ASN B 264 REMARK 465 SER B 314 REMARK 465 ASN B 315 REMARK 465 THR B 316 REMARK 465 LEU B 317 REMARK 465 ARG B 318 REMARK 465 GLY B 319 REMARK 465 ALA B 320 REMARK 465 SER B 321 REMARK 465 ARG B 322 REMARK 465 GLN B 323 REMARK 465 VAL B 368 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 OD1 ASP A 236 NH2 ARG A 286 2.16 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 OG SER B 204 OD1 ASN B 215 8555 2.01 REMARK 500 OD1 ASP B 105 OE2 GLU B 208 8555 2.16 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 ARG A 261 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 261 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 261 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG B 261 NE - CZ - NH1 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 261 NE - CZ - NH2 ANGL. DEV. = 6.2 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 ILE A 40 -66.60 -127.82 REMARK 500 LEU A 69 -35.39 -33.89 REMARK 500 TYR A 96 85.03 46.80 REMARK 500 SER A 97 161.09 174.10 REMARK 500 LEU A 126 -72.97 -113.51 REMARK 500 GLU A 181 74.48 -111.24 REMARK 500 GLU A 182 -19.55 61.12 REMARK 500 LYS A 183 -58.99 -140.20 REMARK 500 LEU A 191 50.60 32.96 REMARK 500 SER A 198 -75.07 -93.05 REMARK 500 GLU A 199 -134.35 42.98 REMARK 500 VAL A 262 -161.19 170.30 REMARK 500 PRO A 263 143.84 -39.37 REMARK 500 ARG A 348 74.23 49.62 REMARK 500 ILE A 349 -0.88 88.55 REMARK 500 ILE B 40 -59.38 -128.82 REMARK 500 LEU B 69 -35.79 -34.15 REMARK 500 TYR B 96 85.69 46.86 REMARK 500 SER B 97 160.72 173.51 REMARK 500 GLU B 181 30.89 -96.96 REMARK 500 GLU B 182 -18.00 84.63 REMARK 500 LYS B 183 -59.65 -139.08 REMARK 500 LEU B 191 49.35 33.79 REMARK 500 ASN B 195 -140.78 57.63 REMARK 500 LEU B 257 -72.15 -53.26 REMARK 500 ARG B 261 74.04 -109.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 182 LYS A 183 149.26 REMARK 500 SER A 201 LEU A 202 -38.19 REMARK 500 GLU B 182 LYS B 183 146.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 3VJJ A 22 368 UNP Q913E4 Q913E4_RBSDV 1 347 DBREF 3VJJ B 22 368 UNP Q913E4 Q913E4_RBSDV 1 347 SEQADV 3VJJ MET A 1 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ SER A 2 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ TYR A 3 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ TYR A 4 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS A 5 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS A 6 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS A 7 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS A 8 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS A 9 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS A 10 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LEU A 11 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ GLY A 12 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ SER A 13 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ THR A 14 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ SER A 15 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LEU A 16 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ TYR A 17 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LYS A 18 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LYS A 19 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ ALA A 20 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ GLY A 21 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LYS A 346 UNP Q913E4 ARG 325 CONFLICT SEQADV 3VJJ MET B 1 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ SER B 2 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ TYR B 3 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ TYR B 4 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS B 5 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS B 6 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS B 7 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS B 8 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS B 9 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ HIS B 10 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LEU B 11 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ GLY B 12 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ SER B 13 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ THR B 14 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ SER B 15 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LEU B 16 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ TYR B 17 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LYS B 18 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LYS B 19 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ ALA B 20 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ GLY B 21 UNP Q913E4 EXPRESSION TAG SEQADV 3VJJ LYS B 346 UNP Q913E4 ARG 325 CONFLICT SEQRES 1 A 368 MET SER TYR TYR HIS HIS HIS HIS HIS HIS LEU GLY SER SEQRES 2 A 368 THR SER LEU TYR LYS LYS ALA GLY MET ALA ASP GLN GLU SEQRES 3 A 368 ARG ARG THR PHE GLY SER TYR LYS ILE GLU GLU LEU THR SEQRES 4 A 368 ILE LYS ASN ASP GLN PRO ASN ARG ASN THR ASN SER SER SEQRES 5 A 368 THR SER GLN SER THR GLU ASN ARG LEU SER THR LYS LYS SEQRES 6 A 368 ILE PRO LEU LEU ASP ASP GLY ILE PHE GLU LEU LEU ASN SEQRES 7 A 368 TYR LEU ILE ASP GLY THR ASN PHE ASP LYS THR CYS TYR SEQRES 8 A 368 CYS GLY PHE ASN TYR SER HIS LEU PRO ASN LEU GLU ARG SEQRES 9 A 368 ASP PHE ASN VAL ALA SER ILE TYR VAL ARG GLU ASN PHE SEQRES 10 A 368 GLU LEU CYS THR GLU ASN LEU ASP LEU LYS ASP TYR ASP SEQRES 11 A 368 ARG GLN ALA ASN ILE SER VAL LYS SER PRO ASP PHE THR SEQRES 12 A 368 LEU LEU LEU GLU TYR THR LEU LYS PRO SER SER GLU THR SEQRES 13 A 368 ASP PRO THR ILE PRO GLU ASN GLU LYS GLU GLU ASN SER SEQRES 14 A 368 LYS PRO VAL THR PRO LYS VAL VAL THR PRO LYS GLU GLU SEQRES 15 A 368 LYS LYS THR VAL GLU MET SER LEU LEU PRO ILE LEU ASN SEQRES 16 A 368 ARG GLU SER GLU GLU SER LEU SER SER GLU ILE LEU GLU SEQRES 17 A 368 GLY GLU ALA ALA VAL VAL ASN VAL PHE LYS MET TYR ILE SEQRES 18 A 368 LYS GLY PHE LEU MET TYR LEU GLY GLU ASN PRO ASN SER SEQRES 19 A 368 TYR ASP ARG GLN LEU ASN ILE GLU LYS TYR ARG PRO LEU SEQRES 20 A 368 LEU ILE SER ILE ILE GLY TYR GLU HIS LEU ILE GLY THR SEQRES 21 A 368 ARG VAL PRO ASN LYS GLU VAL ASN HIS ILE PHE TYR GLN SEQRES 22 A 368 LEU ALA THR PHE ASP ASN TYR PRO PHE ASP LEU LEU ARG SEQRES 23 A 368 PHE GLN LEU SER SER LEU ILE SER THR PRO ALA LEU ILE SEQRES 24 A 368 ARG GLU LYS ILE ALA LYS GLU GLY LEU PHE LYS ILE ILE SEQRES 25 A 368 THR SER ASN THR LEU ARG GLY ALA SER ARG GLN THR VAL SEQRES 26 A 368 LEU PHE ARG GLY ILE ASN GLY SER GLU SER PHE LEU ASN SEQRES 27 A 368 ILE LYS ARG TYR ARG LYS PHE LYS THR ARG ILE VAL GLY SEQRES 28 A 368 ASN VAL ASP CYS VAL ILE LYS SER ASP PHE SER SER LEU SEQRES 29 A 368 LYS LEU ASP VAL SEQRES 1 B 368 MET SER TYR TYR HIS HIS HIS HIS HIS HIS LEU GLY SER SEQRES 2 B 368 THR SER LEU TYR LYS LYS ALA GLY MET ALA ASP GLN GLU SEQRES 3 B 368 ARG ARG THR PHE GLY SER TYR LYS ILE GLU GLU LEU THR SEQRES 4 B 368 ILE LYS ASN ASP GLN PRO ASN ARG ASN THR ASN SER SER SEQRES 5 B 368 THR SER GLN SER THR GLU ASN ARG LEU SER THR LYS LYS SEQRES 6 B 368 ILE PRO LEU LEU ASP ASP GLY ILE PHE GLU LEU LEU ASN SEQRES 7 B 368 TYR LEU ILE ASP GLY THR ASN PHE ASP LYS THR CYS TYR SEQRES 8 B 368 CYS GLY PHE ASN TYR SER HIS LEU PRO ASN LEU GLU ARG SEQRES 9 B 368 ASP PHE ASN VAL ALA SER ILE TYR VAL ARG GLU ASN PHE SEQRES 10 B 368 GLU LEU CYS THR GLU ASN LEU ASP LEU LYS ASP TYR ASP SEQRES 11 B 368 ARG GLN ALA ASN ILE SER VAL LYS SER PRO ASP PHE THR SEQRES 12 B 368 LEU LEU LEU GLU TYR THR LEU LYS PRO SER SER GLU THR SEQRES 13 B 368 ASP PRO THR ILE PRO GLU ASN GLU LYS GLU GLU ASN SER SEQRES 14 B 368 LYS PRO VAL THR PRO LYS VAL VAL THR PRO LYS GLU GLU SEQRES 15 B 368 LYS LYS THR VAL GLU MET SER LEU LEU PRO ILE LEU ASN SEQRES 16 B 368 ARG GLU SER GLU GLU SER LEU SER SER GLU ILE LEU GLU SEQRES 17 B 368 GLY GLU ALA ALA VAL VAL ASN VAL PHE LYS MET TYR ILE SEQRES 18 B 368 LYS GLY PHE LEU MET TYR LEU GLY GLU ASN PRO ASN SER SEQRES 19 B 368 TYR ASP ARG GLN LEU ASN ILE GLU LYS TYR ARG PRO LEU SEQRES 20 B 368 LEU ILE SER ILE ILE GLY TYR GLU HIS LEU ILE GLY THR SEQRES 21 B 368 ARG VAL PRO ASN LYS GLU VAL ASN HIS ILE PHE TYR GLN SEQRES 22 B 368 LEU ALA THR PHE ASP ASN TYR PRO PHE ASP LEU LEU ARG SEQRES 23 B 368 PHE GLN LEU SER SER LEU ILE SER THR PRO ALA LEU ILE SEQRES 24 B 368 ARG GLU LYS ILE ALA LYS GLU GLY LEU PHE LYS ILE ILE SEQRES 25 B 368 THR SER ASN THR LEU ARG GLY ALA SER ARG GLN THR VAL SEQRES 26 B 368 LEU PHE ARG GLY ILE ASN GLY SER GLU SER PHE LEU ASN SEQRES 27 B 368 ILE LYS ARG TYR ARG LYS PHE LYS THR ARG ILE VAL GLY SEQRES 28 B 368 ASN VAL ASP CYS VAL ILE LYS SER ASP PHE SER SER LEU SEQRES 29 B 368 LYS LEU ASP VAL HELIX 1 1 GLY A 72 GLY A 83 1 12 HELIX 2 2 ASN A 85 THR A 89 5 5 HELIX 3 3 ASN A 101 GLU A 122 1 22 HELIX 4 4 LEU A 191 ASN A 195 5 5 HELIX 5 5 SER A 203 GLU A 230 1 28 HELIX 6 6 TYR A 235 LEU A 239 5 5 HELIX 7 7 ILE A 241 LYS A 243 5 3 HELIX 8 8 TYR A 244 ARG A 261 1 18 HELIX 9 9 ASN A 268 PHE A 277 1 10 HELIX 10 10 PRO A 281 LEU A 289 1 9 HELIX 11 11 PRO A 296 GLU A 306 1 11 HELIX 12 12 GLY B 72 GLY B 83 1 12 HELIX 13 13 ASN B 85 THR B 89 5 5 HELIX 14 14 ASN B 101 GLU B 122 1 22 HELIX 15 15 SER B 203 ASN B 231 1 29 HELIX 16 16 TYR B 235 LEU B 239 5 5 HELIX 17 17 ILE B 241 LYS B 243 5 3 HELIX 18 18 TYR B 244 ARG B 261 1 18 HELIX 19 19 ASN B 268 PHE B 277 1 10 HELIX 20 20 PRO B 281 LEU B 289 1 9 HELIX 21 21 PRO B 296 GLU B 306 1 11 SHEET 1 A 2 TYR A 33 LYS A 34 0 SHEET 2 A 2 ASP A 70 ASP A 71 -1 O ASP A 70 N LYS A 34 SHEET 1 B 2 ASN A 168 LYS A 170 0 SHEET 2 B 2 LYS A 340 TYR A 342 -1 O TYR A 342 N ASN A 168 SHEET 1 C 2 VAL A 176 VAL A 177 0 SHEET 2 C 2 MET A 188 SER A 189 -1 O MET A 188 N VAL A 177 SHEET 1 D 2 LYS A 180 GLU A 181 0 SHEET 2 D 2 LYS A 184 THR A 185 -1 O LYS A 184 N GLU A 181 SHEET 1 E 3 PHE A 309 ILE A 311 0 SHEET 2 E 3 VAL A 325 ARG A 328 -1 O LEU A 326 N LYS A 310 SHEET 3 E 3 GLU A 334 PHE A 336 -1 O SER A 335 N PHE A 327 SHEET 1 F 2 TYR B 33 LYS B 34 0 SHEET 2 F 2 ASP B 70 ASP B 71 -1 O ASP B 70 N LYS B 34 SHEET 1 G 2 ASN B 168 LYS B 170 0 SHEET 2 G 2 LYS B 340 TYR B 342 -1 O TYR B 342 N ASN B 168 SHEET 1 H 2 VAL B 176 VAL B 177 0 SHEET 2 H 2 MET B 188 SER B 189 -1 O MET B 188 N VAL B 177 SHEET 1 I 3 PHE B 309 ILE B 311 0 SHEET 2 I 3 VAL B 325 ARG B 328 -1 O LEU B 326 N LYS B 310 SHEET 3 I 3 GLU B 334 PHE B 336 -1 O SER B 335 N PHE B 327 CISPEP 1 ASP A 70 ASP A 71 0 -11.83 CISPEP 2 TYR A 96 SER A 97 0 27.00 CISPEP 3 VAL A 172 THR A 173 0 2.78 CISPEP 4 SER A 290 SER A 291 0 -17.50 CISPEP 5 GLY A 329 ILE A 330 0 -4.89 CISPEP 6 ASP B 70 ASP B 71 0 -13.43 CISPEP 7 TYR B 96 SER B 97 0 27.21 CISPEP 8 VAL B 172 THR B 173 0 3.73 CISPEP 9 SER B 290 SER B 291 0 -18.54 CISPEP 10 GLY B 329 ILE B 330 0 -1.12 CRYST1 127.284 127.284 143.227 90.00 90.00 90.00 P 4 21 2 16 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 0.007856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006982 0.00000