HEADER VIRAL PROTEIN 14-JUN-23 8PEM TITLE ZIKA METHYLTRANSFERASE IN COMPLEX WITH AT-9010 AND SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE NS5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NS5; COMPND 5 EC: 2.1.1.56,2.1.1.57,2.7.7.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZIKA VIRUS; SOURCE 3 ORGANISM_TAXID: 64320; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NTAYA VIRUS, METHYLTRANSFERASE, AT-9010, SAH, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.KREJCOVA,E.BOURA,M.KLIMA REVDAT 1 26-JUN-24 8PEM 0 JRNL AUTH K.KREJCOVA,E.BOURA,M.KLIMA JRNL TITL CRYSTAL STRUCTURE OF ZIKA METHYLTRANSFERASE IN COMPLEX WITH JRNL TITL 2 AT-9010 AND SAH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 14651 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 734 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 28.3800 - 3.4200 0.96 2815 149 0.1932 0.2129 REMARK 3 2 3.4200 - 2.7200 0.97 2790 147 0.2193 0.2690 REMARK 3 3 2.7200 - 2.3700 0.98 2792 147 0.2530 0.2868 REMARK 3 4 2.3700 - 2.1600 0.98 2762 146 0.2651 0.3137 REMARK 3 5 2.1600 - 2.0000 0.96 2758 145 0.2910 0.3457 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) : 0.325 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.323 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.65 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 : 0.002 2090 REMARK 3 ANGLE : 0.446 2834 REMARK 3 CHIRALITY : 0.037 303 REMARK 3 PLANARITY : 0.003 369 REMARK 3 DIHEDRAL : 11.407 794 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 8PEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131173. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-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 : 14679 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.25750 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 1.18100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.240 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 (%): 35.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1M SODIUM HEPES 7.5, REMARK 280 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291.15K 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 20.50800 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 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 GLY A 7 REMARK 465 GLY A 8 REMARK 465 GLY A 9 REMARK 465 THR A 10 REMARK 465 GLY A 11 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 LYS A 17 CD CE NZ REMARK 470 LEU A 28 CG CD1 CD2 REMARK 470 ARG A 43 CB REMARK 470 LYS A 51 CG CD CE REMARK 470 ARG A 63 CD NE CZ NH1 NH2 REMARK 470 HIS A 116 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 133 CD CE NZ REMARK 470 ARG A 203 CD NE CZ NH1 NH2 REMARK 470 ARG A 206 CD NE CZ NH1 NH2 REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 GLN A 244 CB CG CD OE1 NE2 REMARK 470 ARG A 254 CG CD NE CZ NH1 NH2 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 ARG A 181 67.58 60.13 REMARK 500 ARG A 181 67.49 60.39 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 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 156 OG REMARK 620 2 AT9 A 301 O1A 132.3 REMARK 620 3 AT9 A 301 O1B 104.8 94.6 REMARK 620 4 AT9 A 301 O3B 157.7 65.1 55.4 REMARK 620 N 1 2 3 DBREF 8PEM A 7 270 UNP Q32ZE1 POLG_ZIKV 2517 2780 SEQRES 1 A 264 GLY GLY GLY THR GLY GLU THR LEU GLY GLU LYS TRP LYS SEQRES 2 A 264 ALA ARG LEU ASN GLN MET SER ALA LEU GLU PHE TYR SER SEQRES 3 A 264 TYR LYS LYS SER GLY ILE THR GLU VAL CYS ARG GLU GLU SEQRES 4 A 264 ALA ARG ARG ALA LEU LYS ASP GLY VAL ALA THR GLY GLY SEQRES 5 A 264 HIS ALA VAL SER ARG GLY SER ALA LYS ILE ARG TRP LEU SEQRES 6 A 264 GLU GLU ARG GLY TYR LEU GLN PRO TYR GLY LYS VAL VAL SEQRES 7 A 264 ASP LEU GLY CYS GLY ARG GLY GLY TRP SER TYR TYR ALA SEQRES 8 A 264 ALA THR ILE ARG LYS VAL GLN GLU VAL ARG GLY TYR THR SEQRES 9 A 264 LYS GLY GLY PRO GLY HIS GLU GLU PRO MET LEU VAL GLN SEQRES 10 A 264 SER TYR GLY TRP ASN ILE VAL ARG LEU LYS SER GLY VAL SEQRES 11 A 264 ASP VAL PHE HIS MET ALA ALA GLU PRO CYS ASP THR LEU SEQRES 12 A 264 LEU CYS ASP ILE GLY GLU SER SER SER SER PRO GLU VAL SEQRES 13 A 264 GLU GLU THR ARG THR LEU ARG VAL LEU SER MET VAL GLY SEQRES 14 A 264 ASP TRP LEU GLU LYS ARG PRO GLY ALA PHE CYS ILE LYS SEQRES 15 A 264 VAL LEU CYS PRO TYR THR SER THR MET MET GLU THR MET SEQRES 16 A 264 GLU ARG LEU GLN ARG ARG HIS GLY GLY GLY LEU VAL ARG SEQRES 17 A 264 VAL PRO LEU CYS ARG ASN SER THR HIS GLU MET TYR TRP SEQRES 18 A 264 VAL SER GLY ALA LYS SER ASN ILE ILE LYS SER VAL SER SEQRES 19 A 264 THR THR SER GLN LEU LEU LEU GLY ARG MET ASP GLY PRO SEQRES 20 A 264 ARG ARG PRO VAL LYS TYR GLU GLU ASP VAL ASN LEU GLY SEQRES 21 A 264 SER GLY THR ARG HET AT9 A 301 29 HET SAH A 302 26 HET SO4 A 303 5 HET MG A 304 1 HETNAM AT9 [[(2R,3R,4R,5R)-5-(2-AZANYL-6-OXIDANYLIDENE-1H-PURIN-9- HETNAM 2 AT9 YL)-4-FLUORANYL-4-METHYL-3-OXIDANYL-OXOLAN-2- HETNAM 3 AT9 YL]METHOXY-OXIDANYL-PHOSPHORYL] PHOSPHONO HYDROGEN HETNAM 4 AT9 PHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETSYN AT9 AT-9010 FORMUL 2 AT9 C11 H17 F N5 O13 P3 FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 4 SO4 O4 S 2- FORMUL 5 MG MG 2+ FORMUL 6 HOH *90(H2 O) HELIX 1 AA1 THR A 13 MET A 25 1 13 HELIX 2 AA2 SER A 26 LYS A 35 1 10 HELIX 3 AA3 ARG A 43 ASP A 52 1 10 HELIX 4 AA4 ARG A 63 ARG A 74 1 12 HELIX 5 AA5 GLY A 91 ALA A 98 1 8 HELIX 6 AA6 GLY A 126 ASN A 128 5 3 HELIX 7 AA7 ASP A 137 MET A 141 5 5 HELIX 8 AA8 SER A 159 GLU A 179 1 21 HELIX 9 AA9 THR A 194 GLY A 209 1 16 HELIX 10 AB1 ASN A 234 ASP A 251 1 18 SHEET 1 AA1 2 THR A 39 CYS A 42 0 SHEET 2 AA1 2 LYS A 258 GLU A 261 1 O GLU A 260 N CYS A 42 SHEET 1 AA2 7 VAL A 130 LYS A 133 0 SHEET 2 AA2 7 VAL A 103 TYR A 109 1 N GLY A 108 O ARG A 131 SHEET 3 AA2 7 GLY A 81 LEU A 86 1 N VAL A 83 O ARG A 107 SHEET 4 AA2 7 THR A 148 CYS A 151 1 O LEU A 150 N LEU A 86 SHEET 5 AA2 7 ALA A 184 VAL A 189 1 O ALA A 184 N LEU A 149 SHEET 6 AA2 7 MET A 225 VAL A 228 -1 O TRP A 227 N ILE A 187 SHEET 7 AA2 7 GLY A 211 VAL A 213 -1 N VAL A 213 O TYR A 226 LINK OG SER A 156 MG MG A 304 1555 1555 2.54 LINK O1A AT9 A 301 MG MG A 304 1555 1555 2.72 LINK O1B AT9 A 301 MG MG A 304 1555 1555 2.95 LINK O3B AT9 A 301 MG MG A 304 1555 1555 2.46 CRYST1 39.556 41.016 69.035 90.00 96.25 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 0.025281 0.000000 0.002769 0.00000 SCALE2 0.000000 0.024381 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014572 0.00000