HEADER TRANSFERASE 04-AUG-21 7V1E TITLE CRYSTAL STRUCTURE OF OMSK HEMORRHAGIC FEVER VIRUS NS5 MTASE (IN TITLE 2 COMPLEX WITH SAH AND M7GPPPAMG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CORE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENVELOPE PROTEIN E,FLAVIVIRIN PROTEASE NS2B REGULATORY COMPND 5 SUBUNIT,FLAVIVIRIN PROTEASE NS3 CATALYTIC SUBUNIT,GENOME POLYPROTEIN, COMPND 6 MATRIX PROTEIN,NON-STRUCTURAL PROTEIN 1,NON-STRUCTURAL PROTEIN 2A, COMPND 7 NON-STRUCTURAL PROTEIN 2B,NON-STRUCTURAL PROTEIN 3,NON-STRUCTURAL COMPND 8 PROTEIN 4A,NON-STRUCTURAL PROTEIN 4B,PEPTIDE 2K,PEPTIDE PR,PROTEIN COMPND 9 PRM,RNA-DIRECTED RNA POLYMERASE NS5,SERINE PROTEASE NS3,SERINE COMPND 10 PROTEASE SUBUNIT NS2B,SMALL ENVELOPE PROTEIN M; COMPND 11 EC: 3.4.21.91,3.6.1.15,3.6.4.13; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OMSK HEMORRHAGIC FEVER VIRUS; SOURCE 3 ORGANISM_COMMON: OHFV; SOURCE 4 ORGANISM_TAXID: 12542; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS GUANYLYLTRANSFERASE, METHYLTRANSFERASE, VIRAL PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.JIA,P.GONG REVDAT 4 29-NOV-23 7V1E 1 REMARK REVDAT 3 10-AUG-22 7V1E 1 JRNL REVDAT 2 13-JUL-22 7V1E 1 JRNL REVDAT 1 15-JUN-22 7V1E 0 JRNL AUTH H.JIA,Y.ZHONG,C.PENG,P.GONG JRNL TITL CRYSTAL STRUCTURES OF FLAVIVIRUS NS5 GUANYLYLTRANSFERASE JRNL TITL 2 REVEAL A GMP-ARGININE ADDUCT. JRNL REF J.VIROL. V. 96 41822 2022 JRNL REFN ESSN 1098-5514 JRNL PMID 35758665 JRNL DOI 10.1128/JVI.00418-22 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.7 REMARK 3 NUMBER OF REFLECTIONS : 33228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1691 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 20.4800 - 3.6400 0.97 2968 148 0.1813 0.1879 REMARK 3 2 3.6300 - 2.8900 0.94 2863 117 0.1842 0.2117 REMARK 3 3 2.8900 - 2.5200 0.99 2993 150 0.2008 0.2200 REMARK 3 4 2.5200 - 2.2900 1.00 2985 186 0.1983 0.2376 REMARK 3 5 2.2900 - 2.1300 0.95 2868 150 0.2054 0.2767 REMARK 3 6 2.1300 - 2.0000 1.00 2986 159 0.2065 0.2491 REMARK 3 7 2.0000 - 1.9000 0.98 2900 171 0.2153 0.2866 REMARK 3 8 1.9000 - 1.8200 0.91 2704 171 0.2298 0.2388 REMARK 3 9 1.8200 - 1.7500 0.82 2405 135 0.2275 0.2734 REMARK 3 10 1.7500 - 1.6900 0.72 2188 118 0.2146 0.2243 REMARK 3 11 1.6900 - 1.6400 0.65 1940 100 0.1978 0.2352 REMARK 3 12 1.6400 - 1.5900 0.58 1737 86 0.2118 0.2634 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.82 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7V1E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1300022316. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.42500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 4K6M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ISOPROPANOL, TRISODIUM CITRATE, PEG REMARK 280 4000, GLYCEROL, PH 5.6, EVAPORATION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 45.19800 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 HIS A 265 REMARK 465 HIS A 266 REMARK 465 HIS A 267 REMARK 465 HIS A 268 REMARK 465 HIS A 269 REMARK 465 HIS A 270 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 22 CG CD OE1 OE2 REMARK 470 LYS A 39 CG CD CE NZ REMARK 470 LYS A 108 CG CD CE NZ REMARK 470 GLN A 136 CG CD OE1 NE2 REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 ARG A 198 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 248 CG CD OE1 NE2 REMARK 470 ARG A 249 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 253 CG CD NE CZ NH1 NH2 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 605 DISTANCE = 6.67 ANGSTROMS DBREF 7V1E A 7 264 UNP C4TPE0 C4TPE0_OHFV 2518 2775 SEQADV 7V1E MET A 6 UNP C4TPE0 INITIATING METHIONINE SEQADV 7V1E HIS A 265 UNP C4TPE0 EXPRESSION TAG SEQADV 7V1E HIS A 266 UNP C4TPE0 EXPRESSION TAG SEQADV 7V1E HIS A 267 UNP C4TPE0 EXPRESSION TAG SEQADV 7V1E HIS A 268 UNP C4TPE0 EXPRESSION TAG SEQADV 7V1E HIS A 269 UNP C4TPE0 EXPRESSION TAG SEQADV 7V1E HIS A 270 UNP C4TPE0 EXPRESSION TAG SEQRES 1 A 265 MET THR LEU GLY ASP LEU TRP LYS ARG ARG LEU ASN ASN SEQRES 2 A 265 CYS THR LYS GLU GLU PHE PHE ALA TYR ARG ARG THR GLY SEQRES 3 A 265 ILE LEU GLU THR GLU ARG ASP LYS ALA ARG GLU LEU LEU SEQRES 4 A 265 ARG LYS GLY GLU THR ASN MET GLY LEU ALA VAL SER ARG SEQRES 5 A 265 GLY THR ALA LYS LEU ALA TRP LEU GLU GLU ARG GLY TYR SEQRES 6 A 265 VAL ASN LEU LYS GLY GLU VAL VAL ASP LEU GLY CYS GLY SEQRES 7 A 265 ARG GLY GLY TRP SER TYR TYR ALA ALA SER ARG PRO ALA SEQRES 8 A 265 VAL MET GLY VAL LYS ALA TYR THR ILE GLY GLY LYS GLY SEQRES 9 A 265 HIS GLU ALA PRO LYS MET VAL THR SER LEU GLY TRP ASN SEQRES 10 A 265 LEU ILE LYS PHE ARG ALA GLY MET ASP VAL PHE THR MET SEQRES 11 A 265 GLN PRO HIS ARG ALA ASP THR VAL MET CYS ASP ILE GLY SEQRES 12 A 265 GLU SER SER PRO ASP ALA ALA ILE GLU GLY GLU ARG THR SEQRES 13 A 265 ARG LYS VAL ILE LEU LEU MET GLU GLN TRP LYS ASN ARG SEQRES 14 A 265 ASN PRO SER ALA SER CYS VAL PHE LYS VAL LEU ALA PRO SEQRES 15 A 265 TYR ARG PRO GLU VAL ILE GLU ALA LEU HIS ARG PHE GLN SEQRES 16 A 265 LEU GLN TRP GLY GLY GLY LEU VAL ARG THR PRO PHE SER SEQRES 17 A 265 ARG ASN SER THR HIS GLU MET TYR TYR SER THR ALA ILE SEQRES 18 A 265 SER GLY ASN ILE VAL ASN SER VAL ASN VAL GLN SER ARG SEQRES 19 A 265 LYS LEU LEU ALA ARG PHE GLY ASP GLN ARG GLY PRO ILE SEQRES 20 A 265 ARG VAL PRO GLU MET ASP LEU GLY VAL GLY THR ARG HIS SEQRES 21 A 265 HIS HIS HIS HIS HIS HET GOL A 301 6 HET SAH A 302 26 HET V9G A 303 104 HET 5GP A 304 46 HETNAM GOL GLYCEROL HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM V9G 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)- HETNAM 2 V9G ADENOSINE HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 4 V9G C22 H32 N10 O17 P3 FORMUL 5 5GP C10 H14 N5 O8 P FORMUL 6 HOH *205(H2 O) HELIX 1 AA1 THR A 7 CYS A 19 1 13 HELIX 2 AA2 THR A 20 THR A 30 1 11 HELIX 3 AA3 ARG A 37 GLY A 47 1 11 HELIX 4 AA4 ARG A 57 ARG A 68 1 12 HELIX 5 AA5 GLY A 85 SER A 93 1 9 HELIX 6 AA6 GLY A 120 ASN A 122 5 3 HELIX 7 AA7 ASP A 131 MET A 135 5 5 HELIX 8 AA8 ASP A 153 ASN A 175 1 23 HELIX 9 AA9 ARG A 189 GLY A 204 1 16 HELIX 10 AB1 ASN A 229 ALA A 243 1 15 SHEET 1 AA1 2 LEU A 33 GLU A 36 0 SHEET 2 AA1 2 ILE A 252 PRO A 255 1 O ILE A 252 N GLU A 34 SHEET 1 AA2 7 ILE A 124 ALA A 128 0 SHEET 2 AA2 7 VAL A 97 THR A 104 1 N VAL A 100 O LYS A 125 SHEET 3 AA2 7 GLY A 75 LEU A 80 1 N VAL A 77 O GLY A 99 SHEET 4 AA2 7 THR A 142 CYS A 145 1 O MET A 144 N LEU A 80 SHEET 5 AA2 7 SER A 179 VAL A 184 1 O SER A 179 N VAL A 143 SHEET 6 AA2 7 MET A 220 SER A 223 -1 O MET A 220 N VAL A 184 SHEET 7 AA2 7 GLY A 206 VAL A 208 -1 N VAL A 208 O TYR A 221 LINK O16AV9G A 303 P A5GP A 304 1555 1555 1.61 LINK O16BV9G A 303 P B5GP A 304 1555 1555 1.61 CRYST1 35.073 90.396 45.366 90.00 90.77 90.00 P 1 21 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 0.028512 0.000000 0.000383 0.00000 SCALE2 0.000000 0.011062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022045 0.00000