HEADER VIRUS 03-APR-23 8IXW TITLE TILAPIA LAKE VIRUS S8 SEGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHAINS: A,B; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TILAPIA LAKE VIRUS; SOURCE 3 ORGANISM_TAXID: 1549864; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TILAPIA LAKE VIRUS, S8 SEGMENT, VIRUS EXPDTA X-RAY DIFFRACTION AUTHOR Z.X.WANG,Y.A.ZHANG,S.Y.OUYANG REVDAT 1 10-APR-24 8IXW 0 JRNL AUTH Z.X.WANG,Y.A.ZHANG JRNL TITL STRUCTURE AND FUNCTION OF TILAPIA LAKE VIRUS S8 SEGMENT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 38262 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1905 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 20.9600 - 4.3300 0.96 2655 67 0.1604 0.1866 REMARK 3 2 4.3300 - 3.4400 0.97 2641 105 0.1566 0.1649 REMARK 3 3 3.4400 - 3.0100 0.97 2713 40 0.1763 0.2432 REMARK 3 4 3.0100 - 2.7300 0.97 2600 154 0.1724 0.1965 REMARK 3 5 2.7300 - 2.5400 0.97 2624 125 0.1793 0.2096 REMARK 3 6 2.5400 - 2.3900 0.97 2589 125 0.1856 0.1826 REMARK 3 7 2.3900 - 2.2700 0.96 2582 185 0.1867 0.1990 REMARK 3 8 2.2700 - 2.1700 0.96 2564 178 0.1861 0.2281 REMARK 3 9 2.1700 - 2.0900 0.96 2588 155 0.1949 0.1983 REMARK 3 10 2.0900 - 2.0100 0.96 2588 133 0.1989 0.2523 REMARK 3 11 2.0100 - 1.9500 0.97 2591 131 0.2163 0.2218 REMARK 3 12 1.9500 - 1.8900 0.96 2601 147 0.2180 0.2003 REMARK 3 13 1.8900 - 1.8500 0.96 2510 200 0.2137 0.2679 REMARK 3 14 1.8400 - 1.8000 0.95 2511 160 0.2287 0.3021 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) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.059 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.15 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 2643 REMARK 3 ANGLE : 0.865 3549 REMARK 3 CHIRALITY : 0.044 427 REMARK 3 PLANARITY : 0.006 453 REMARK 3 DIHEDRAL : 4.823 355 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8IXW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036710. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 298.15 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) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38281 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.03903 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21110 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08 M POTASSIUM CHLORIDE, 0.02 M REMARK 280 BARIUM CHLORIDE DIHYDRATE, 0.04 M SODIUM CACODYLATE TRIHYDRATE REMARK 280 PH 6.0, 40% V/V (+/-)-2-METHYL-2,4-PENTANEDIOL, 0.012 M SPERMINE REMARK 280 TETRAHYDROCHLORIDE., VAPOR DIFFUSION, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 8 REMARK 465 GLU A 9 REMARK 465 GLY A 10 REMARK 465 GLN A 11 REMARK 465 GLY A 12 REMARK 465 LYS A 13 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 ILE B 4 REMARK 465 PRO B 5 REMARK 465 THR B 6 REMARK 465 LEU B 7 REMARK 465 ARG B 8 REMARK 465 GLU B 9 REMARK 465 GLY B 10 REMARK 465 GLN B 11 REMARK 465 GLY B 12 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 358 O HOH B 418 1.88 REMARK 500 O HOH A 421 O HOH A 423 1.89 REMARK 500 O HOH A 414 O HOH A 416 1.94 REMARK 500 O HOH A 319 O HOH A 338 1.96 REMARK 500 OD2 ASP B 44 O HOH B 301 1.98 REMARK 500 O HOH A 359 O HOH A 415 1.99 REMARK 500 O HOH A 438 O HOH B 458 2.00 REMARK 500 O HOH B 416 O HOH B 431 2.04 REMARK 500 OE1 GLU B 171 NZ LYS B 174 2.10 REMARK 500 O HOH B 345 O HOH B 417 2.11 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 15 81.26 9.24 REMARK 500 THR B 148 9.52 -68.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 443 DISTANCE = 5.83 ANGSTROMS DBREF1 8IXW A 1 174 UNP A0A1Y9SHR5_9VIRU DBREF2 8IXW A A0A1Y9SHR5 1 174 DBREF1 8IXW B 1 174 UNP A0A1Y9SHR5_9VIRU DBREF2 8IXW B A0A1Y9SHR5 1 174 SEQRES 1 A 174 MET ALA GLN ILE PRO THR LEU ARG GLU GLY GLN GLY LYS SEQRES 2 A 174 LEU TYR ASP PHE THR LEU ASN GLY MET THR VAL THR ARG SEQRES 3 A 174 ASP THR VAL ASN THR VAL VAL ALA LEU GLU PHE LEU VAL SEQRES 4 A 174 ASN ALA SER PRO ASP LEU LEU SER LEU THR ILE GLY GLU SEQRES 5 A 174 GLY LEU SER GLU GLU THR LYS PHE LYS HIS LEU LEU VAL SEQRES 6 A 174 LYS HIS ALA GLY MET THR ARG LYS ARG ILE GLU GLU ARG SEQRES 7 A 174 LEU GLY ARG ILE SER ARG ARG VAL SER VAL THR VAL ASP SEQRES 8 A 174 ALA ILE ILE ILE THR ASN ARG LYS GLY GLN ARG PHE GLU SEQRES 9 A 174 PHE ASN ARG LYS GLN TYR LEU ASP ILE ALA LYS GLN ALA SEQRES 10 A 174 MET LYS LEU LYS LEU PRO GLY ILE ASN CYS VAL ASP ILE SEQRES 11 A 174 PRO THR ALA LEU ALA PHE LEU GLU GLU VAL LEU ALA THR SEQRES 12 A 174 ALA LEU LYS ASP THR GLU GLY SER GLN ASP ASP ARG MET SEQRES 13 A 174 ALA LEU LYS ALA ASP THR SER ALA ALA ILE ASN HIS PHE SEQRES 14 A 174 ARG GLU MET LEU LYS SEQRES 1 B 174 MET ALA GLN ILE PRO THR LEU ARG GLU GLY GLN GLY LYS SEQRES 2 B 174 LEU TYR ASP PHE THR LEU ASN GLY MET THR VAL THR ARG SEQRES 3 B 174 ASP THR VAL ASN THR VAL VAL ALA LEU GLU PHE LEU VAL SEQRES 4 B 174 ASN ALA SER PRO ASP LEU LEU SER LEU THR ILE GLY GLU SEQRES 5 B 174 GLY LEU SER GLU GLU THR LYS PHE LYS HIS LEU LEU VAL SEQRES 6 B 174 LYS HIS ALA GLY MET THR ARG LYS ARG ILE GLU GLU ARG SEQRES 7 B 174 LEU GLY ARG ILE SER ARG ARG VAL SER VAL THR VAL ASP SEQRES 8 B 174 ALA ILE ILE ILE THR ASN ARG LYS GLY GLN ARG PHE GLU SEQRES 9 B 174 PHE ASN ARG LYS GLN TYR LEU ASP ILE ALA LYS GLN ALA SEQRES 10 B 174 MET LYS LEU LYS LEU PRO GLY ILE ASN CYS VAL ASP ILE SEQRES 11 B 174 PRO THR ALA LEU ALA PHE LEU GLU GLU VAL LEU ALA THR SEQRES 12 B 174 ALA LEU LYS ASP THR GLU GLY SER GLN ASP ASP ARG MET SEQRES 13 B 174 ALA LEU LYS ALA ASP THR SER ALA ALA ILE ASN HIS PHE SEQRES 14 B 174 ARG GLU MET LEU LYS HET SEY A 201 8 HET SEY A 202 8 HET SEY A 203 8 HET SEY A 204 8 HET SEY B 201 8 HET SEY B 202 8 HETNAM SEY SELENOUREA FORMUL 3 SEY 6(C H4 N2 SE) FORMUL 9 HOH *303(H2 O) HELIX 1 AA1 THR A 25 ALA A 41 1 17 HELIX 2 AA2 SER A 42 GLY A 51 1 10 HELIX 3 AA3 SER A 55 GLY A 69 1 15 HELIX 4 AA4 THR A 71 SER A 83 1 13 HELIX 5 AA5 ARG A 107 LYS A 119 1 13 HELIX 6 AA6 ASP A 129 ASP A 147 1 19 HELIX 7 AA7 SER A 151 LYS A 174 1 24 HELIX 8 AA8 THR B 25 ALA B 41 1 17 HELIX 9 AA9 SER B 42 GLY B 51 1 10 HELIX 10 AB1 SER B 55 GLY B 69 1 15 HELIX 11 AB2 THR B 71 SER B 83 1 13 HELIX 12 AB3 ARG B 107 MET B 118 1 12 HELIX 13 AB4 ASP B 129 ASP B 147 1 19 HELIX 14 AB5 SER B 151 MET B 172 1 22 SHEET 1 AA1 2 PHE A 17 LEU A 19 0 SHEET 2 AA1 2 MET A 22 VAL A 24 -1 O MET A 22 N LEU A 19 SHEET 1 AA2 3 VAL A 86 VAL A 88 0 SHEET 2 AA2 3 ALA A 92 THR A 96 -1 O ILE A 94 N SER A 87 SHEET 3 AA2 3 ARG A 102 ASN A 106 -1 O PHE A 103 N ILE A 95 SHEET 1 AA3 2 PHE B 17 LEU B 19 0 SHEET 2 AA3 2 MET B 22 VAL B 24 -1 O MET B 22 N LEU B 19 SHEET 1 AA4 3 VAL B 86 VAL B 88 0 SHEET 2 AA4 3 ALA B 92 THR B 96 -1 O ILE B 94 N SER B 87 SHEET 3 AA4 3 ARG B 102 ASN B 106 -1 O PHE B 103 N ILE B 95 CRYST1 50.486 51.342 52.706 106.87 108.92 108.02 P 1 2 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 0.019807 0.006444 0.010640 0.00000 SCALE2 0.000000 0.020482 0.009867 0.00000 SCALE3 0.000000 0.000000 0.022263 0.00000