HEADER HYDROLASE 24-SEP-12 4H9J TITLE CRYSTAL STRUCTURE OF N-TERMINAL PROTEASE (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 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, CYSTEINE KEYWDS 2 PROTEASE, IRF-3 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 2 24-JAN-18 4H9J 1 AUTHOR REVDAT 1 30-OCT-13 4H9J 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) : 29.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 17961 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1664 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 29.6903 - 3.6610 1.00 1470 156 0.1657 0.2085 REMARK 3 2 3.6610 - 2.9067 1.00 1388 144 0.1651 0.2019 REMARK 3 3 2.9067 - 2.5395 1.00 1362 138 0.1940 0.1922 REMARK 3 4 2.5395 - 2.3074 1.00 1361 144 0.1773 0.2350 REMARK 3 5 2.3074 - 2.1420 1.00 1348 141 0.1678 0.1864 REMARK 3 6 2.1420 - 2.0158 1.00 1358 129 0.1630 0.2193 REMARK 3 7 2.0158 - 1.9149 1.00 1348 142 0.1696 0.2095 REMARK 3 8 1.9149 - 1.8315 1.00 1326 134 0.1636 0.2204 REMARK 3 9 1.8315 - 1.7610 1.00 1328 125 0.1732 0.2128 REMARK 3 10 1.7610 - 1.7002 1.00 1355 151 0.1727 0.2147 REMARK 3 11 1.7002 - 1.6471 1.00 1334 126 0.1727 0.2017 REMARK 3 12 1.6471 - 1.6000 1.00 1319 134 0.1794 0.2285 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.870 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 : 0.007 1155 REMARK 3 ANGLE : 1.123 1567 REMARK 3 CHIRALITY : 0.082 166 REMARK 3 PLANARITY : 0.005 203 REMARK 3 DIHEDRAL : 12.250 432 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 4H9J 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_1000075189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MULTILAYER CONFOCAL REMARK 200 OPTICS : MULTILAYER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROTEUM PLUS PLUS REMARK 200 DATA SCALING SOFTWARE : PROTEUM PLUS PLUS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 29.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 34.32 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04200 REMARK 200 FOR THE DATA SET : 12.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31800 REMARK 200 FOR SHELL : 1.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2 M (NH4)2SO4 AND 0.1 M REMARK 280 HEPES, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 30.06650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.69900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.06650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.69900 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 HIS A 17 REMARK 465 MET A 18 REMARK 465 GLY A 19 REMARK 465 VAL A 20 REMARK 465 ARG A 65 REMARK 465 LYS A 66 REMARK 465 GLY A 67 REMARK 465 ASP A 68 REMARK 465 CYS A 69 REMARK 465 ARG A 70 REMARK 465 SER A 71 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 OG1 THR A 59 ND2 ASN A 62 2.09 REMARK 500 O HOH A 345 O HOH A 412 2.11 REMARK 500 NZ LYS A 153 O HOH A 393 2.14 REMARK 500 O HOH A 242 O HOH A 398 2.14 REMARK 500 O HOH A 372 O HOH A 381 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 369 O HOH A 392 3445 2.05 REMARK 500 O HOH A 251 O HOH A 393 3444 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4H9K RELATED DB: PDB DBREF 4H9J A 18 168 UNP Q68871 Q68871_9FLAV 18 168 SEQADV 4H9J GLY A 15 UNP Q68871 EXPRESSION TAG SEQADV 4H9J SER A 16 UNP Q68871 EXPRESSION TAG SEQADV 4H9J HIS A 17 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 CYS FORMUL 2 HOH *224(H2 O) HELIX 1 1 THR A 59 LEU A 63 5 5 HELIX 2 2 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 ALA A 109 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 2.04 CISPEP 1 LEU A 47 PRO A 48 0 1.88 CISPEP 2 GLY A 86 PRO A 87 0 2.53 CRYST1 60.133 65.398 33.315 90.00 90.00 90.00 P 21 21 2 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 0.016630 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030017 0.00000