HEADER VIRAL PROTEIN 15-OCT-22 8BC5 TITLE RECOMBINANT TIPULA OLERACEA NUDIVIRUS POLYHEDRIN - SELENOMETHIONINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MOBP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TIPULA OLERACEA NUDIVIRUS; SOURCE 3 ORGANISM_TAXID: 1546257; SOURCE 4 GENE: MOBP, TONV_059; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS NUDIVIRUS, POLYHEDRA, OCCLUSION BODY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.R.KEOWN,J.M.GRIMES REVDAT 2 24-JAN-24 8BC5 1 JRNL REMARK REVDAT 1 12-JUL-23 8BC5 0 JRNL AUTH J.R.KEOWN,A.D.CRAWSHAW,J.TRINCAO,L.CARRIQUE,R.J.GILDEA, JRNL AUTH 2 S.HORRELL,A.J.WARREN,D.AXFORD,R.OWEN,G.EVANS,A.BEZIER, JRNL AUTH 3 P.METCALF,J.M.GRIMES JRNL TITL ATOMIC STRUCTURE OF A NUDIVIRUS OCCLUSION BODY PROTEIN JRNL TITL 2 DETERMINED FROM A 70-YEAR-OLD CRYSTAL SAMPLE. JRNL REF NAT COMMUN V. 14 4160 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37443157 JRNL DOI 10.1038/S41467-023-39819-1 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 13233 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 671 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 42.3900 - 3.2700 1.00 2803 149 0.1751 0.2224 REMARK 3 2 3.2700 - 2.5900 1.00 2678 143 0.1571 0.1964 REMARK 3 3 2.5900 - 2.2600 1.00 2634 141 0.1522 0.1970 REMARK 3 4 2.2600 - 2.0600 0.80 2103 111 0.1611 0.2046 REMARK 3 5 2.0600 - 1.9100 0.89 2344 127 0.2139 0.2967 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.183 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.359 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.61 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 : 0.005 1744 REMARK 3 ANGLE : 0.769 2371 REMARK 3 CHIRALITY : 0.042 278 REMARK 3 PLANARITY : 0.007 297 REMARK 3 DIHEDRAL : 5.176 230 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 8BC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292126106. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-21 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 : DIAMOND REMARK 200 BEAMLINE : VMXM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2.MULTIPLEX REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13277 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 42.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 51.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.7 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 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CRANK REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: IN CELL CRYSTALLISATION, TEMPERATURE REMARK 280 301K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 70.16533 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 35.08267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.08267 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 70.16533 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MSE A 1 REMARK 465 GLY A 2 REMARK 465 TYR A 3 REMARK 465 LEU A 4 REMARK 465 CYS A 5 REMARK 465 ASN A 6 REMARK 465 ASP A 7 REMARK 465 TYR A 8 REMARK 465 GLY A 9 REMARK 465 GLY A 165 REMARK 465 ILE A 166 REMARK 465 CYS A 167 REMARK 465 TYR A 168 REMARK 465 GLY A 169 REMARK 465 GLU A 170 REMARK 465 LYS A 171 REMARK 465 ASP A 172 REMARK 465 TYR A 173 REMARK 465 ASN A 174 REMARK 465 ARG A 175 REMARK 465 PHE A 176 REMARK 465 GLU A 177 REMARK 465 LEU A 236 REMARK 465 THR A 237 REMARK 465 LYS A 238 REMARK 465 VAL A 239 REMARK 465 CYS A 240 REMARK 465 CYS A 241 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 N TYR A 178 O HOH A 401 2.05 REMARK 500 O HOH A 493 O HOH A 495 2.07 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 32 -18.29 82.84 REMARK 500 THR A 93 -45.39 72.53 REMARK 500 THR A 98 -125.96 -139.88 REMARK 500 ASP A 182 87.27 -157.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 140 O REMARK 620 2 ASP A 140 OD1 70.6 REMARK 620 3 ASN A 143 OD1 76.7 111.9 REMARK 620 4 ASN A 148 O 110.0 82.6 165.5 REMARK 620 5 HOH A 425 O 140.2 145.4 72.8 95.1 REMARK 620 6 HOH A 435 O 75.4 133.4 89.6 80.1 79.4 REMARK 620 N 1 2 3 4 5 DBREF1 8BC5 A 1 241 UNP A0A0B4VFQ3_9VIRU DBREF2 8BC5 A A0A0B4VFQ3 1 241 SEQADV 8BC5 MSE A 104 UNP A0A0B4VFQ PHE 104 ENGINEERED MUTATION SEQADV 8BC5 MSE A 105 UNP A0A0B4VFQ LEU 105 ENGINEERED MUTATION SEQADV 8BC5 MSE A 137 UNP A0A0B4VFQ LEU 137 ENGINEERED MUTATION SEQRES 1 A 241 MSE GLY TYR LEU CYS ASN ASP TYR GLY TYR GLU PRO ASN SEQRES 2 A 241 VAL ASP TYR PRO ASN ALA SER HIS ALA GLY LEU TYR ASP SEQRES 3 A 241 ARG SER LYS GLN PRO TYR VAL ASP THR ALA ILE GLY PRO SEQRES 4 A 241 LYS THR THR ILE GLN PHE ASP HIS VAL PHE ILE LYS SER SEQRES 5 A 241 ASP PHE LYS THR TRP LEU ALA HIS ASN GLN ASP GLU ALA SEQRES 6 A 241 ILE LEU LEU ILE ARG LEU TYR GLU LEU GLY LEU LEU LEU SEQRES 7 A 241 GLN GLY ARG SER ASP SER PHE LEU GLU PHE TYR ASN ASN SEQRES 8 A 241 THR THR TYR ILE THR ARG THR ASP SER LYS GLN PRO MSE SEQRES 9 A 241 MSE ASN LYS TYR GLY LYS LEU VAL ASP THR THR SER VAL SEQRES 10 A 241 THR CYS LEU ASP ILE PHE LEU SER VAL VAL LEU PHE ALA SEQRES 11 A 241 LEU ASN GLN ILE ASP SER MSE ILE CYS ASP PHE LYS ASN SEQRES 12 A 241 THR PRO TRP ILE ASN LEU SER LYS GLU HIS LYS LYS ILE SEQRES 13 A 241 TYR GLU LEU VAL ARG GLY ILE PHE GLY ILE CYS TYR GLY SEQRES 14 A 241 GLU LYS ASP TYR ASN ARG PHE GLU TYR CYS PRO PHE ASP SEQRES 15 A 241 ALA ASN SER THR ALA SER ALA LEU ASN VAL ASN ALA THR SEQRES 16 A 241 LEU ASN ALA LYS LYS THR ILE GLU LEU ILE THR CYS GLY SEQRES 17 A 241 LEU ILE ARG ALA LEU ILE ALA TYR ALA ASN LEU VAL THR SEQRES 18 A 241 ALA PHE SER ALA ASP LYS THR ALA LEU LEU HIS GLU ILE SEQRES 19 A 241 LEU LEU THR LYS VAL CYS CYS HET MSE A 104 17 HET MSE A 105 17 HET MSE A 137 17 HET CA A 301 1 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 CA CA 2+ FORMUL 3 HOH *98(H2 O) HELIX 1 AA1 GLU A 11 TYR A 16 1 6 HELIX 2 AA2 TYR A 16 HIS A 21 1 6 HELIX 3 AA3 TYR A 32 ALA A 36 5 5 HELIX 4 AA4 GLY A 38 LYS A 40 5 3 HELIX 5 AA5 SER A 52 ASN A 61 1 10 HELIX 6 AA6 ASN A 61 GLN A 79 1 19 HELIX 7 AA7 ARG A 81 GLU A 87 1 7 HELIX 8 AA8 LYS A 101 ASP A 113 1 13 HELIX 9 AA9 SER A 116 ASN A 143 1 28 HELIX 10 AB1 SER A 150 PHE A 164 1 15 HELIX 11 AB2 ASP A 182 ASN A 184 5 3 HELIX 12 AB3 SER A 185 LEU A 235 1 51 SHEET 1 AA1 2 THR A 42 PHE A 45 0 SHEET 2 AA1 2 VAL A 48 LYS A 51 -1 O ILE A 50 N ILE A 43 SSBOND 1 CYS A 119 CYS A 179 1555 1665 2.03 LINK C PRO A 103 N MSE A 104 1555 1555 1.33 LINK C MSE A 104 N MSE A 105 1555 1555 1.33 LINK C MSE A 105 N ASN A 106 1555 1555 1.33 LINK C SER A 136 N MSE A 137 1555 1555 1.33 LINK C MSE A 137 N ILE A 138 1555 1555 1.34 LINK O ASP A 140 CA CA A 301 1555 1555 2.47 LINK OD1 ASP A 140 CA CA A 301 1555 1555 2.47 LINK OD1 ASN A 143 CA CA A 301 1555 1555 2.49 LINK O ASN A 148 CA CA A 301 1555 1555 2.34 LINK CA CA A 301 O HOH A 425 1555 1555 2.51 LINK CA CA A 301 O HOH A 435 1555 1555 2.64 CRYST1 53.481 53.481 105.248 90.00 90.00 120.00 P 32 2 1 6 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 0.018698 0.010795 0.000000 0.00000 SCALE2 0.000000 0.021591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009501 0.00000