HEADER TRANSFERASE 22-FEB-22 7Z05 TITLE WHITE BREAM VIRUS N7-METHYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NSP1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: WHITE BREAM VIRUS; SOURCE 3 ORGANISM_TAXID: 405554; SOURCE 4 STRAIN: ISOLATE BLICCA BJOERKNA L./GERMANY/DF24/00; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS N7-METHYL TRANSFERASE, CAPPING ENZYME, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.SHANNON,P.GAUFFRE,B.CANARD,F.FERRON REVDAT 4 01-MAY-24 7Z05 1 REMARK REVDAT 3 16-NOV-22 7Z05 1 JRNL REVDAT 2 02-NOV-22 7Z05 1 JRNL REVDAT 1 28-SEP-22 7Z05 0 JRNL AUTH A.SHANNON,B.SAMA,P.GAUFFRE,T.GUEZ,F.DEBART,J.J.VASSEUR, JRNL AUTH 2 E.DECROLY,B.CANARD,F.FERRON JRNL TITL A SECOND TYPE OF N7-GUANINE RNA CAP METHYLTRANSFERASE IN AN JRNL TITL 2 UNUSUAL LOCUS OF A LARGE RNA VIRUS GENOME. JRNL REF NUCLEIC ACIDS RES. V. 50 11186 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 36265859 JRNL DOI 10.1093/NAR/GKAC876 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 11998 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 586 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 52.1300 - 3.6900 0.99 2920 141 0.1859 0.2362 REMARK 3 2 3.6900 - 2.9300 1.00 2842 153 0.2115 0.2552 REMARK 3 3 2.9300 - 2.5600 1.00 2837 147 0.2423 0.3238 REMARK 3 4 2.5600 - 2.3300 1.00 2813 145 0.2945 0.3486 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.27 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 7Z05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292121298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.992 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20200131 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 52.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.92400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: ALPHA FOLD 2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 20.3 % PEG 3350, 0.2 M REMARK 280 MGCL AND 10% ISOPROPANOL, PH 7.7, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 52.60800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.89350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 52.60800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.89350 REMARK 290 SMTRY3 4 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 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 ASP A 1 REMARK 465 LYS A 2 REMARK 465 LEU A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 GLN A 6 REMARK 465 ASP A 7 REMARK 465 TYR A 8 REMARK 465 ASN A 9 REMARK 465 THR A 10 REMARK 465 ASP A 11 REMARK 465 PHE A 12 REMARK 465 ILE A 13 REMARK 465 TYR A 14 REMARK 465 GLU A 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 ARG A 19 REMARK 465 GLN A 20 REMARK 465 PRO A 21 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 GLU A 23 80.57 -165.72 REMARK 500 PRO A 70 75.97 -66.73 REMARK 500 ASN A 89 45.91 -142.82 REMARK 500 LYS A 98 78.13 -100.59 REMARK 500 SER A 120 -38.90 -135.54 REMARK 500 GLU A 166 -128.05 52.56 REMARK 500 THR A 174 -99.61 57.74 REMARK 500 GLU A 177 79.40 -114.80 REMARK 500 THR A 212 127.19 -38.42 REMARK 500 LYS A 251 -16.81 -41.99 REMARK 500 VAL A 252 41.73 -69.20 REMARK 500 TRP A 258 0.02 -58.44 REMARK 500 LEU A 259 62.33 -107.77 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 474 DISTANCE = 6.03 ANGSTROMS DBREF 7Z05 A 1 260 UNP Q008X6 R1AB_WBV24 1374 1633 SEQRES 1 A 260 ASP LYS LEU THR GLN GLN ASP TYR ASN THR ASP PHE ILE SEQRES 2 A 260 TYR GLU SER HIS HIS ARG GLN PRO LYS GLU SER LEU THR SEQRES 3 A 260 HIS ALA SER VAL LEU SER ALA TYR THR ALA SER TYR LYS SEQRES 4 A 260 THR THR ALA ILE LYS SER ILE ALA ASP ASN ALA VAL VAL SEQRES 5 A 260 LEU ASP ILE GLY TYR GLY LYS GLY ASN ASP GLY PRO ARG SEQRES 6 A 260 TYR ALA VAL ARG PRO LEU THR VAL THR GLY ILE ASP THR SEQRES 7 A 260 ALA ALA ARG MET LEU ALA ILE ALA ASP GLN ASN LYS PRO SEQRES 8 A 260 GLU ASN VAL THR LEU VAL LYS GLN GLY PHE PHE THR HIS SEQRES 9 A 260 ILE THR LYS THR SER ASN THR TYR THR HIS VAL ILE ALA SEQRES 10 A 260 PHE ASN SER LEU HIS TYR PRO LEU ALA SER SER HIS PRO SEQRES 11 A 260 ASP THR LEU VAL GLN ARG LEU PRO THR CYS PRO ALA ASN SEQRES 12 A 260 ILE LEU ILE PRO CYS HIS HIS LEU LEU GLU GLY ILE GLN SEQRES 13 A 260 THR PRO THR TYR SER VAL VAL LYS ASP GLU ASP MET TRP SEQRES 14 A 260 CYS VAL LYS VAL THR LYS ASN GLU PHE ILE GLU SER SER SEQRES 15 A 260 TYR ASN TYR ASP VAL PHE VAL LYS ALA LEU GLU SER LYS SEQRES 16 A 260 TYR HIS VAL THR ILE GLY SER LEU LEU ASP CYS VAL GLU SEQRES 17 A 260 LYS PRO SER THR ARG SER ILE THR PRO THR LEU TRP THR SEQRES 18 A 260 ALA MET ARG ASN PHE VAL ASN ASN ASP GLN GLU MET GLN SEQRES 19 A 260 ARG ILE LEU SER GLY TYR ILE THR PHE ASN LEU THR PRO SEQRES 20 A 260 LEU PRO PRO LYS VAL GLU ILE ILE ASN ASP TRP LEU ASP HET SAH A 301 26 HET PEG A 302 7 HET PEG A 303 7 HET NA A 304 1 HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NA SODIUM ION FORMUL 2 SAH C14 H20 N6 O5 S FORMUL 3 PEG 2(C4 H10 O3) FORMUL 5 NA NA 1+ FORMUL 6 HOH *74(H2 O) HELIX 1 AA1 THR A 26 ILE A 46 1 21 HELIX 2 AA2 ASP A 62 VAL A 68 1 7 HELIX 3 AA3 ALA A 79 GLN A 88 1 10 HELIX 4 AA4 GLY A 100 THR A 108 1 9 HELIX 5 AA5 TYR A 123 SER A 128 5 6 HELIX 6 AA6 HIS A 129 LEU A 137 1 9 HELIX 7 AA7 HIS A 149 LEU A 152 5 4 HELIX 8 AA8 ASN A 184 LYS A 195 1 12 HELIX 9 AA9 LEU A 204 CYS A 206 5 3 HELIX 10 AB1 THR A 216 ASN A 229 1 14 HELIX 11 AB2 ASP A 230 GLY A 239 1 10 HELIX 12 AB3 GLU A 253 TRP A 258 1 6 SHEET 1 AA1 7 VAL A 94 VAL A 97 0 SHEET 2 AA1 7 THR A 72 ILE A 76 1 N GLY A 75 O THR A 95 SHEET 3 AA1 7 VAL A 51 ILE A 55 1 N VAL A 52 O THR A 72 SHEET 4 AA1 7 HIS A 114 PHE A 118 1 O ILE A 116 N LEU A 53 SHEET 5 AA1 7 ALA A 142 PRO A 147 1 O LEU A 145 N ALA A 117 SHEET 6 AA1 7 TYR A 240 PRO A 247 -1 O ILE A 241 N ILE A 146 SHEET 7 AA1 7 TYR A 196 SER A 202 -1 N HIS A 197 O THR A 246 SHEET 1 AA2 3 TYR A 160 ASP A 165 0 SHEET 2 AA2 3 MET A 168 VAL A 173 -1 O MET A 168 N ASP A 165 SHEET 3 AA2 3 ASN A 176 SER A 181 -1 O GLU A 180 N TRP A 169 CRYST1 105.216 49.787 53.926 90.00 97.72 90.00 C 1 2 1 4 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 0.009504 0.000000 0.001289 0.00000 SCALE2 0.000000 0.020086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018714 0.00000