HEADER HYDROLASE 24-SEP-12 4H9K TITLE CRYSTAL STRUCTURE OF CLEAVAGE SITE MUTANT OF NPRO OF CLASSICAL SWINE TITLE 2 FEVER VIRUS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOG CHOLERA VIRUS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLASSICAL SWINE FEVER VIRUS; SOURCE 3 ORGANISM_TAXID: 358769; SOURCE 4 STRAIN: ALFORT/187; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (ROSETTA-DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS NPRO, CSFV, AUTOPROTEASE, PESTIVIRUS, CYSTEINE PROTEASE, IRF-3 KEYWDS 2 ANTAGONIST, IRF-3, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.GOTTIPATI,N.RUGGLI,M.GERBER,J.-D.TRATSCHIN,M.BENNING,H.BELLAMY, AUTHOR 2 K.H.CHOI REVDAT 3 20-SEP-23 4H9K 1 REMARK SEQADV LINK REVDAT 2 24-JAN-18 4H9K 1 AUTHOR REVDAT 1 30-OCT-13 4H9K 0 JRNL AUTH K.GOTTIPATI,N.RUGGLI,M.GERBER,J.D.TRATSCHIN,M.BENNING, JRNL AUTH 2 H.BELLAMY,K.H.CHOI JRNL TITL THE STRUCTURE OF CLASSICAL SWINE FEVER VIRUS N(PRO): A NOVEL JRNL TITL 2 CYSTEINE AUTOPROTEASE AND ZINC-BINDING PROTEIN INVOLVED IN JRNL TITL 3 SUBVERSION OF TYPE I INTERFERON INDUCTION. JRNL REF PLOS PATHOG. V. 9 03704 2013 JRNL REFN ISSN 1553-7366 JRNL PMID 24146623 JRNL DOI 10.1371/JOURNAL.PPAT.1003704 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 23012 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.690 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 37.7425 - 3.8519 1.00 1752 167 0.1743 0.2000 REMARK 3 2 3.8519 - 3.0578 1.00 1666 159 0.1651 0.2134 REMARK 3 3 3.0578 - 2.6714 1.00 1638 155 0.1936 0.2277 REMARK 3 4 2.6714 - 2.4272 1.00 1624 154 0.1838 0.2074 REMARK 3 5 2.4272 - 2.2533 1.00 1624 156 0.1742 0.2272 REMARK 3 6 2.2533 - 2.1204 1.00 1618 153 0.1749 0.2248 REMARK 3 7 2.1204 - 2.0142 1.00 1621 154 0.1832 0.2108 REMARK 3 8 2.0142 - 1.9266 1.00 1602 153 0.1728 0.2095 REMARK 3 9 1.9266 - 1.8524 1.00 1613 154 0.1875 0.1891 REMARK 3 10 1.8524 - 1.7885 1.00 1590 152 0.1933 0.2396 REMARK 3 11 1.7885 - 1.7326 1.00 1588 150 0.1898 0.2554 REMARK 3 12 1.7326 - 1.6830 0.96 1552 148 0.1895 0.2234 REMARK 3 13 1.6830 - 1.6387 0.65 1035 99 0.1957 0.2647 REMARK 3 14 1.6387 - 1.5987 0.31 489 46 0.1974 0.2050 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1210 REMARK 3 ANGLE : 1.055 1641 REMARK 3 CHIRALITY : 0.074 172 REMARK 3 PLANARITY : 0.005 210 REMARK 3 DIHEDRAL : 12.807 446 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 4H9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 85 REMARK 200 PH : 7.5 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NONE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24710 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 37.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03700 REMARK 200 FOR THE DATA SET : 40.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.45200 REMARK 200 FOR SHELL : 1.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4H9J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2 M (NH4)2SO4 AND 0.1 M REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K 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 20.74450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.73200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.14900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.73200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.74450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.14900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 15 REMARK 465 SER A 16 REMARK 465 LYS A 145 REMARK 465 ARG A 146 REMARK 465 GLY A 147 REMARK 465 GLU A 148 REMARK 465 PRO A 149 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 O2 SO4 A 201 O HOH A 538 2.11 REMARK 500 O HOH A 386 O HOH A 488 2.18 REMARK 500 O HOH A 371 O HOH A 433 2.19 REMARK 500 O HOH A 453 O HOH A 497 2.19 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 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 49 NE2 REMARK 620 2 CYS A 69 SG 120.0 REMARK 620 3 ALA A 168 OXT 97.9 109.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4H9J RELATED DB: PDB DBREF 4H9K A 18 167 UNP Q68871 Q68871_9FLAV 18 167 SEQADV 4H9K GLY A 15 UNP Q68871 EXPRESSION TAG SEQADV 4H9K SER A 16 UNP Q68871 EXPRESSION TAG SEQADV 4H9K HIS A 17 UNP Q68871 EXPRESSION TAG SEQADV 4H9K ALA A 168 UNP Q68871 EXPRESSION TAG SEQRES 1 A 154 GLY SER HIS MET GLY VAL GLU GLU PRO VAL TYR ASP ALA SEQRES 2 A 154 THR GLY LYS PRO LEU PHE GLY ASP PRO SER GLU VAL HIS SEQRES 3 A 154 PRO GLN SER THR LEU LYS LEU PRO HIS ASP ARG GLY ARG SEQRES 4 A 154 GLY ASN ILE LYS THR THR LEU LYS ASN LEU PRO ARG LYS SEQRES 5 A 154 GLY ASP CYS ARG SER GLY ASN HIS LEU GLY PRO VAL SER SEQRES 6 A 154 GLY ILE TYR VAL LYS PRO GLY PRO VAL PHE TYR GLN ASP SEQRES 7 A 154 TYR MET GLY PRO VAL TYR HIS ARG ALA PRO LEU GLU PHE SEQRES 8 A 154 PHE SER GLU ALA GLN PHE CYS GLU VAL THR LYS ARG ILE SEQRES 9 A 154 GLY ARG VAL THR GLY SER ASP GLY ARG LEU TYR HIS ILE SEQRES 10 A 154 TYR VAL CYS ILE ASP GLY CYS ILE LEU LEU LYS LEU ALA SEQRES 11 A 154 LYS ARG GLY GLU PRO ARG THR LEU LYS TRP ILE ARG ASN SEQRES 12 A 154 PHE THR ASP CYS PRO LEU TRP VAL THR SER ALA HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET ZN A 204 1 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *262(H2 O) HELIX 1 1 PRO A 102 GLU A 104 5 3 SHEET 1 A 4 ILE A 56 THR A 58 0 SHEET 2 A 4 VAL A 88 ASP A 92 -1 O GLN A 91 N ILE A 56 SHEET 3 A 4 GLY A 80 LYS A 84 -1 N LYS A 84 O VAL A 88 SHEET 4 A 4 LEU A 163 SER A 167 -1 O LEU A 163 N VAL A 83 SHEET 1 B 5 PHE A 106 GLU A 108 0 SHEET 2 B 5 THR A 151 TRP A 154 -1 O LYS A 153 N SER A 107 SHEET 3 B 5 ILE A 139 LEU A 143 -1 N LEU A 141 O LEU A 152 SHEET 4 B 5 LEU A 128 CYS A 134 -1 N HIS A 130 O LYS A 142 SHEET 5 B 5 THR A 115 THR A 122 -1 N VAL A 121 O TYR A 129 SSBOND 1 CYS A 112 CYS A 134 1555 1555 2.02 LINK NE2 HIS A 49 ZN ZN A 204 1555 1555 2.06 LINK SG CYS A 69 ZN ZN A 204 1555 1555 2.27 LINK OXT ALA A 168 ZN ZN A 204 1555 1555 1.91 CISPEP 1 LEU A 47 PRO A 48 0 1.22 CISPEP 2 GLY A 86 PRO A 87 0 -3.65 SITE 1 AC1 4 LYS A 116 ARG A 156 HOH A 389 HOH A 538 SITE 1 AC2 5 HIS A 40 ARG A 127 LEU A 128 HOH A 406 SITE 2 AC2 5 HOH A 452 SITE 1 AC3 4 LYS A 66 ARG A 120 HOH A 390 HOH A 478 SITE 1 AC4 4 HIS A 49 CYS A 69 HIS A 74 ALA A 168 CRYST1 41.489 58.298 75.464 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 0.024103 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017153 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013251 0.00000