HEADER VIRAL PROTEIN 23-SEP-17 5YGH TITLE CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM ZIKA VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZIKA VIRUS (STRAIN MR 766); SOURCE 3 ORGANISM_COMMON: ZIKV; SOURCE 4 ORGANISM_TAXID: 64320; SOURCE 5 STRAIN: MR 766; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS ZIKA VIRUS, CAPSID (C), RNA BINDING PROTEIN, VIRUS ASSEMBLY, VIRAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.SHANG,H.SONG,Y.SHI,J.QI,G.F.GAO REVDAT 3 22-NOV-23 5YGH 1 REMARK REVDAT 2 04-APR-18 5YGH 1 JRNL REVDAT 1 28-FEB-18 5YGH 0 JRNL AUTH Z.SHANG,H.SONG,Y.SHI,J.QI,G.F.GAO JRNL TITL CRYSTAL STRUCTURE OF THE CAPSID PROTEIN FROM ZIKA VIRUS. JRNL REF J. MOL. BIOL. V. 430 948 2018 JRNL REFN ESSN 1089-8638 JRNL PMID 29454707 JRNL DOI 10.1016/J.JMB.2018.02.006 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.8 REMARK 3 NUMBER OF REFLECTIONS : 10989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 526 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 29.7962 - 2.9900 0.97 3049 137 0.2060 0.2107 REMARK 3 2 2.9900 - 2.3736 0.99 3054 144 0.2035 0.2442 REMARK 3 3 2.3736 - 2.0736 0.81 2446 149 0.2037 0.2449 REMARK 3 4 2.0736 - 1.8840 0.62 1914 96 0.2214 0.2429 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.880 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 : 0.006 1150 REMARK 3 ANGLE : 0.841 1534 REMARK 3 CHIRALITY : 0.040 176 REMARK 3 PLANARITY : 0.005 184 REMARK 3 DIHEDRAL : 14.426 448 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 19.3592-121.2956 5.6997 REMARK 3 T TENSOR REMARK 3 T11: 0.0600 T22: 0.0805 REMARK 3 T33: 0.0463 T12: 0.0011 REMARK 3 T13: 0.0018 T23: -0.0260 REMARK 3 L TENSOR REMARK 3 L11: 2.9658 L22: 1.4943 REMARK 3 L33: 1.7281 L12: 0.9015 REMARK 3 L13: 0.0317 L23: -0.1375 REMARK 3 S TENSOR REMARK 3 S11: 0.0189 S12: 0.2850 S13: -0.3833 REMARK 3 S21: 0.0406 S22: -0.0346 S23: -0.0200 REMARK 3 S31: 0.0733 S32: -0.0172 S33: -0.0222 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 25.9778-117.3740 10.0262 REMARK 3 T TENSOR REMARK 3 T11: 0.0724 T22: 0.0619 REMARK 3 T33: 0.0458 T12: -0.0067 REMARK 3 T13: -0.0187 T23: 0.0143 REMARK 3 L TENSOR REMARK 3 L11: 1.9735 L22: 1.8697 REMARK 3 L33: 1.5072 L12: 0.4563 REMARK 3 L13: 0.0037 L23: 0.5779 REMARK 3 S TENSOR REMARK 3 S11: 0.0897 S12: -0.0961 S13: -0.0898 REMARK 3 S21: 0.2120 S22: -0.1017 S23: -0.1879 REMARK 3 S31: 0.0892 S32: 0.0847 S33: 0.0217 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 5YGH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7293 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13611 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 16.00 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1370 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 16.70 REMARK 200 R MERGE FOR SHELL (I) : 0.74300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.401 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: 1SFK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M IRON (III) CHLORIDE HEXAHYDRATE, REMARK 280 0.1M SODIUM CITRATE PH5.6, 10% V/V JEFFAMINE M-600, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.03500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 29.03500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.03500 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: 4660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 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 ARG A 23 REMARK 465 VAL A 24 REMARK 465 SER A 25 REMARK 465 ARG B 23 REMARK 465 VAL B 24 REMARK 465 SER B 25 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 O HOH B 119 O HOH B 139 1.88 REMARK 500 NZ LYS B 60 O HOH B 101 1.95 REMARK 500 OE1 GLU B 79 NZ LYS B 82 2.00 REMARK 500 O HOH B 139 O HOH B 144 2.06 REMARK 500 REMARK 500 REMARK: NULL DBREF1 5YGH A 23 98 UNP A0A1S6Q290_ZIKV DBREF2 5YGH A A0A1S6Q290 23 98 DBREF1 5YGH B 23 98 UNP A0A1S6Q290_ZIKV DBREF2 5YGH B A0A1S6Q290 23 98 SEQRES 1 A 76 ARG VAL SER PRO PHE GLY GLY LEU LYS ARG LEU PRO ALA SEQRES 2 A 76 GLY LEU LEU LEU GLY HIS GLY PRO ILE ARG MET VAL LEU SEQRES 3 A 76 ALA ILE LEU ALA PHE LEU ARG PHE THR ALA ILE LYS PRO SEQRES 4 A 76 SER LEU GLY LEU ILE ASN ARG TRP GLY SER VAL GLY LYS SEQRES 5 A 76 LYS GLU ALA MET GLU ILE ILE LYS LYS PHE LYS LYS ASP SEQRES 6 A 76 LEU ALA ALA MET LEU ARG ILE ILE ASN ALA ARG SEQRES 1 B 76 ARG VAL SER PRO PHE GLY GLY LEU LYS ARG LEU PRO ALA SEQRES 2 B 76 GLY LEU LEU LEU GLY HIS GLY PRO ILE ARG MET VAL LEU SEQRES 3 B 76 ALA ILE LEU ALA PHE LEU ARG PHE THR ALA ILE LYS PRO SEQRES 4 B 76 SER LEU GLY LEU ILE ASN ARG TRP GLY SER VAL GLY LYS SEQRES 5 B 76 LYS GLU ALA MET GLU ILE ILE LYS LYS PHE LYS LYS ASP SEQRES 6 B 76 LEU ALA ALA MET LEU ARG ILE ILE ASN ALA ARG FORMUL 3 HOH *87(H2 O) HELIX 1 AA1 GLY A 36 GLY A 40 5 5 HELIX 2 AA2 PRO A 43 THR A 57 1 15 HELIX 3 AA3 SER A 62 VAL A 72 1 11 HELIX 4 AA4 GLY A 73 ARG A 98 1 26 HELIX 5 AA5 GLY B 36 GLY B 40 5 5 HELIX 6 AA6 PRO B 43 THR B 57 1 15 HELIX 7 AA7 SER B 62 VAL B 72 1 11 HELIX 8 AA8 GLY B 73 ALA B 97 1 25 CRYST1 69.417 69.417 58.070 90.00 90.00 120.00 P 63 12 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 0.014406 0.008317 0.000000 0.00000 SCALE2 0.000000 0.016634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017221 0.00000