HEADER VIRAL PROTEIN 16-MAY-22 7XT3 TITLE CRYSTAL STRUCTURE OF HEPATITIS VIRUS A 2C PROTEIN 128-335 AA COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: DEPOSITOR REFERENCE: GB NP_740555.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATOVIRUS A; SOURCE 3 ORGANISM_TAXID: 12092; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS VIRAL PROTEIN, NONSTRUCTURAL PROTEIN 2C EXPDTA X-RAY DIFFRACTION AUTHOR P.CHEN,J.A.WOJDYLA,Z.LI,M.WANG,S.CUI REVDAT 4 23-NOV-22 7XT3 1 JRNL REVDAT 3 24-AUG-22 7XT3 1 JRNL REVDAT 2 17-AUG-22 7XT3 1 JRNL REVDAT 1 27-JUL-22 7XT3 0 JRNL AUTH P.CHEN,J.A.WOJDYLA,O.COLASANTI,Z.LI,B.QIN,M.WANG,V.LOHMANN, JRNL AUTH 2 S.CUI JRNL TITL BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF HEPATITIS A JRNL TITL 2 VIRUS 2C REVEALS AN UNUSUAL RIBONUCLEASE ACTIVITY ON JRNL TITL 3 SINGLE-STRANDED RNA. JRNL REF NUCLEIC ACIDS RES. V. 50 9470 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35947700 JRNL DOI 10.1093/NAR/GKAC671 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24647 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1221 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 43.2900 - 4.4800 1.00 2600 134 0.2045 0.2449 REMARK 3 2 4.4800 - 3.5500 1.00 2593 130 0.1797 0.1864 REMARK 3 3 3.5500 - 3.1100 1.00 2630 137 0.2114 0.2929 REMARK 3 4 3.1000 - 2.8200 1.00 2596 137 0.2141 0.2568 REMARK 3 5 2.8200 - 2.6200 1.00 2598 134 0.2481 0.2709 REMARK 3 6 2.6200 - 2.4600 1.00 2594 138 0.2711 0.2794 REMARK 3 7 2.4600 - 2.3400 1.00 2624 135 0.2866 0.3250 REMARK 3 8 2.3400 - 2.2400 1.00 2576 137 0.3226 0.3239 REMARK 3 9 2.2400 - 2.1500 0.99 2615 139 0.3595 0.4547 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) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.62 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: NATIVE-SAD REMARK 4 REMARK 4 7XT3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029534. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.1-4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24694 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 43.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.305 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.78900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.810 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 200 CUBIC CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.45 MM AMMONIUM PHOSPHATE MONOBASIC, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.08250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.83300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.34350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.83300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.08250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.34350 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 GLN A 128 REMARK 465 ALA A 129 REMARK 465 MET A 130 REMARK 465 VAL A 131 REMARK 465 THR A 132 REMARK 465 ARG A 133 REMARK 465 CYS A 134 REMARK 465 GLN A 198 REMARK 465 ASN A 199 REMARK 465 THR A 200 REMARK 465 THR A 201 REMARK 465 MET A 221 REMARK 465 ALA A 222 REMARK 465 SER A 223 REMARK 465 LEU A 224 REMARK 465 GLU A 225 REMARK 465 GLU A 226 REMARK 465 LYS A 227 REMARK 465 GLY A 228 REMARK 465 ARG A 229 REMARK 465 HIS A 230 REMARK 465 PHE A 231 REMARK 465 PRO A 245 REMARK 465 SER A 246 REMARK 465 PRO A 247 REMARK 465 LYS A 248 REMARK 465 THR A 249 REMARK 465 VAL A 250 REMARK 465 TYR A 251 REMARK 465 VAL A 252 REMARK 465 LYS A 253 REMARK 465 GLU A 254 REMARK 465 ALA A 255 REMARK 465 ILE A 256 REMARK 465 ASP A 257 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 O HOH A 532 O HOH A 534 1.97 REMARK 500 O HOH A 525 O HOH A 539 2.00 REMARK 500 O HOH A 535 O HOH A 538 2.19 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 ASP A 180 30.34 -89.76 REMARK 500 SER A 186 37.93 -144.58 REMARK 500 ILE A 196 96.11 -66.69 REMARK 500 ARG A 218 -155.41 -113.77 REMARK 500 LEU A 219 73.84 -156.66 REMARK 500 SER A 243 -162.18 -78.46 REMARK 500 ARG A 259 -154.67 -119.74 REMARK 500 ASP A 278 34.57 -87.50 REMARK 500 ASN A 325 72.30 -102.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GRB RELATED DB: PDB REMARK 900 EV71 2C PROTEIN COMPLEXED WITH ATP-GAMA-S REMARK 900 RELATED ID: 5GQ1 RELATED DB: PDB REMARK 900 EV71 2C ATPASE REMARK 900 RELATED ID: 5Z3Q RELATED DB: PDB REMARK 900 PV 2C ATPASE DBREF 7XT3 A 128 335 UNP G4W9T5 G4W9T5_9PICO 1215 1422 SEQRES 1 A 208 GLN ALA MET VAL THR ARG CYS GLU PRO VAL VAL CYS TYR SEQRES 2 A 208 LEU TYR GLY LYS ARG GLY GLY GLY LYS SER LEU THR SER SEQRES 3 A 208 ILE ALA LEU ALA THR LYS ILE CYS LYS HIS TYR GLY VAL SEQRES 4 A 208 GLU PRO GLU LYS ASN ILE TYR THR LYS PRO VAL ALA SER SEQRES 5 A 208 ASP TYR TRP ASP GLY TYR SER GLY GLN LEU VAL CYS ILE SEQRES 6 A 208 ILE ASP ASP ILE GLY GLN ASN THR THR ASP GLU ASP TRP SEQRES 7 A 208 SER ASP PHE CYS GLN LEU VAL SER GLY CYS PRO MET ARG SEQRES 8 A 208 LEU ASN MET ALA SER LEU GLU GLU LYS GLY ARG HIS PHE SEQRES 9 A 208 SER SER PRO PHE ILE ILE ALA THR SER ASN TRP SER ASN SEQRES 10 A 208 PRO SER PRO LYS THR VAL TYR VAL LYS GLU ALA ILE ASP SEQRES 11 A 208 ARG ARG LEU HIS PHE LYS VAL GLU VAL LYS PRO ALA SER SEQRES 12 A 208 PHE PHE LYS ASN PRO HIS ASN ASP MET LEU ASN VAL ASN SEQRES 13 A 208 LEU ALA LYS THR ASN ASP ALA ILE LYS ASP MET SER CYS SEQRES 14 A 208 VAL ASP LEU ILE MET ASP GLY HIS ASN VAL SER LEU MET SEQRES 15 A 208 ASP LEU LEU SER SER LEU VAL MET THR VAL GLU ILE ARG SEQRES 16 A 208 LYS GLN ASN MET THR GLU PHE MET GLU LEU TRP SER GLN HET PO4 A 401 5 HET PO4 A 402 5 HET PO4 A 403 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 3(O4 P 3-) FORMUL 5 HOH *40(H2 O) HELIX 1 AA1 GLY A 148 TYR A 164 1 17 HELIX 2 AA2 GLU A 167 LYS A 170 5 4 HELIX 3 AA3 ASP A 204 GLY A 214 1 11 HELIX 4 AA4 SER A 270 LYS A 273 5 4 HELIX 5 AA5 ASN A 281 ASN A 288 1 8 HELIX 6 AA6 SER A 307 GLN A 324 1 18 HELIX 7 AA7 MET A 326 GLN A 335 1 10 SHEET 1 AA1 7 ILE A 172 PRO A 176 0 SHEET 2 AA1 7 VAL A 190 ILE A 196 1 O ILE A 192 N TYR A 173 SHEET 3 AA1 7 PHE A 235 SER A 240 1 O ILE A 237 N CYS A 191 SHEET 4 AA1 7 VAL A 138 TYR A 142 1 N LEU A 141 O ALA A 238 SHEET 5 AA1 7 HIS A 261 PRO A 268 1 O PHE A 262 N TYR A 140 SHEET 6 AA1 7 VAL A 297 MET A 301 -1 O ASP A 298 N LYS A 267 SHEET 7 AA1 7 HIS A 304 VAL A 306 -1 O VAL A 306 N LEU A 299 CRYST1 50.165 54.687 85.666 90.00 90.00 90.00 P 21 21 21 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 0.019934 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018286 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011673 0.00000