HEADER VIRAL PROTEIN 29-AUG-23 8QDJ TITLE NTAYA VIRUS METHYLTRANSFERASE IN COMPLEX WIH SINEFUNGIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NTAYA VIRUS METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NTAYA VIRUS METHYLTRANSFERASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NTAYA VIRUS; SOURCE 3 ORGANISM_TAXID: 64292; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS FLAVIVIRUS, NTAYA VIRUS, SINEFUNGIN, METHYLTRANSFERASE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.KREJCOVA,E.BOURA,M.KLIMA REVDAT 1 04-SEP-24 8QDJ 0 JRNL AUTH K.KREJCOVA,P.KRAFCIKOVA,M.KLIMA,D.CHALUPSKA,K.CHALUPSKY, JRNL AUTH 2 E.ZILECKA,E.BOURA JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS IN FLAVIVIRUS NS5 JRNL TITL 2 PROTEINS GAINED BY THE STRUCTURE OF NTAYA VIRUS POLYMERASE JRNL TITL 3 AND METHYLTRANSFERASE. JRNL REF STRUCTURE V. 32 1099 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38781970 JRNL DOI 10.1016/J.STR.2024.04.020 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 25123 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 26.0700 - 4.3300 1.00 1698 147 0.1571 0.1567 REMARK 3 2 4.3300 - 3.4400 1.00 1664 141 0.1486 0.1669 REMARK 3 3 3.4400 - 3.0100 1.00 1641 153 0.1710 0.1966 REMARK 3 4 3.0100 - 2.7300 1.00 1654 141 0.1872 0.2345 REMARK 3 5 2.7300 - 2.5400 1.00 1661 144 0.1823 0.2313 REMARK 3 6 2.5400 - 2.3900 1.00 1654 136 0.1753 0.1950 REMARK 3 7 2.3900 - 2.2700 1.00 1667 142 0.1709 0.2471 REMARK 3 8 2.2700 - 2.1700 1.00 1646 143 0.1651 0.1964 REMARK 3 9 2.1700 - 2.0900 1.00 1645 140 0.1717 0.2400 REMARK 3 10 2.0900 - 2.0100 0.99 1614 136 0.1774 0.2225 REMARK 3 11 2.0100 - 1.9500 1.00 1676 136 0.1858 0.2663 REMARK 3 12 1.9500 - 1.8900 1.00 1631 156 0.1887 0.2324 REMARK 3 13 1.8900 - 1.8500 1.00 1651 133 0.2080 0.2671 REMARK 3 14 1.8400 - 1.8000 1.00 1631 142 0.2279 0.2749 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) : 0.188 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.741 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.89 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 2114 REMARK 3 ANGLE : 0.770 2856 REMARK 3 CHIRALITY : 0.049 303 REMARK 3 PLANARITY : 0.008 372 REMARK 3 DIHEDRAL : 12.403 806 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 8QDJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54187 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 26.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.19910 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3500 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.110 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M BIS-TRI 5.5, 25 % PEG 3350, VAPOR DIFFUSION, TEMPERATURE REMARK 280 291K 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 35.54600 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: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 ARG A 7 CD NE CZ NH1 NH2 REMARK 470 GLU A 27 CD OE1 OE2 REMARK 470 LYS A 73 CD CE NZ REMARK 470 LYS A 96 CD CE NZ REMARK 470 LYS A 106 CD CE NZ REMARK 470 GLN A 140 CG CD OE1 NE2 REMARK 470 GLU A 171 CD OE1 OE2 REMARK 470 LYS A 198 CG CD CE NZ DBREF 8QDJ A 6 266 UNP K0BRZ6 K0BRZ6_9FLAV 2527 2787 SEQRES 1 A 261 GLY ARG MET LEU GLY GLU MET TRP LYS ALA GLN LEU ASN SEQRES 2 A 261 GLN LEU THR ARG GLN GLU PHE MET GLU TYR ARG ARG ASP SEQRES 3 A 261 GLY ILE ILE GLU VAL ASP ARG SER ALA ALA ARG LYS ALA SEQRES 4 A 261 ARG ARG GLU GLY ASN VAL THR GLY GLY HIS PRO VAL SER SEQRES 5 A 261 ARG GLY THR ALA LYS LEU ARG TRP MET VAL GLU ARG GLY SEQRES 6 A 261 PHE VAL LYS PRO HIS GLY LYS VAL ILE ASP LEU GLY CYS SEQRES 7 A 261 GLY ARG GLY GLY TRP SER TYR TYR CYS ALA THR LEU LYS SEQRES 8 A 261 LEU VAL GLN GLU VAL LYS GLY TYR THR LYS GLY GLY PRO SEQRES 9 A 261 GLY HIS GLU GLU PRO VAL MET MET GLN SER TYR GLY TRP SEQRES 10 A 261 ASN LEU VAL SER LEU LYS SER GLY VAL ASP VAL PHE TYR SEQRES 11 A 261 ARG PRO SER GLU GLN SER ASP THR LEU LEU CYS ASP ILE SEQRES 12 A 261 GLY GLU ALA SER PRO VAL PRO GLU ILE GLU GLU ALA ARG SEQRES 13 A 261 THR VAL LYS VAL LEU GLN MET VAL GLU GLU TRP LEU SER SEQRES 14 A 261 ARG GLY VAL GLU ASP PHE CYS VAL LYS ILE LEU CYS PRO SEQRES 15 A 261 TYR MET PRO LYS VAL LEU LYS GLU LEU GLU LYS MET GLN SEQRES 16 A 261 LEU ARG TRP GLY GLY GLY LEU ILE ARG VAL PRO LEU SER SEQRES 17 A 261 ARG ASN SER ASN HIS GLU MET TYR TRP VAL SER GLY ALA SEQRES 18 A 261 SER GLY ASN ILE THR ASN SER VAL ASN THR VAL SER GLN SEQRES 19 A 261 MET LEU ILE ASN ARG MET ASN ARG THR ASN ARG ASN GLY SEQRES 20 A 261 PRO LYS TYR GLU GLU ASP VAL HIS LEU GLY SER GLY THR SEQRES 21 A 261 ARG HET SFG A 301 27 HET SO4 A 302 5 HETNAM SFG SINEFUNGIN HETNAM SO4 SULFATE ION HETSYN SFG ADENOSYL-ORNITHINE FORMUL 2 SFG C15 H23 N7 O5 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *240(H2 O) HELIX 1 AA1 MET A 8 LEU A 20 1 13 HELIX 2 AA2 THR A 21 ARG A 30 1 10 HELIX 3 AA3 ARG A 38 GLY A 48 1 11 HELIX 4 AA4 ARG A 58 ARG A 69 1 12 HELIX 5 AA5 GLY A 86 THR A 94 1 9 HELIX 6 AA6 GLY A 121 ASN A 123 5 3 HELIX 7 AA7 ASP A 132 ARG A 136 5 5 HELIX 8 AA8 VAL A 154 SER A 174 1 21 HELIX 9 AA9 MET A 189 GLY A 204 1 16 HELIX 10 AB1 ASN A 229 ASN A 246 1 18 SHEET 1 AA1 2 ILE A 34 ASP A 37 0 SHEET 2 AA1 2 LYS A 254 GLU A 257 1 O LYS A 254 N GLU A 35 SHEET 1 AA2 7 VAL A 125 LYS A 128 0 SHEET 2 AA2 7 VAL A 98 TYR A 104 1 N VAL A 101 O SER A 126 SHEET 3 AA2 7 GLY A 76 LEU A 81 1 N VAL A 78 O GLU A 100 SHEET 4 AA2 7 THR A 143 CYS A 146 1 O LEU A 145 N LEU A 81 SHEET 5 AA2 7 ASP A 179 ILE A 184 1 O LYS A 183 N CYS A 146 SHEET 6 AA2 7 MET A 220 VAL A 223 -1 O MET A 220 N ILE A 184 SHEET 7 AA2 7 GLY A 206 ILE A 208 -1 N GLY A 206 O VAL A 223 CRYST1 38.389 71.092 50.445 90.00 92.70 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 0.026049 0.000000 0.001228 0.00000 SCALE2 0.000000 0.014066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019846 0.00000