HEADER VIRAL PROTEIN 26-AUG-22 8GPH TITLE CRYSTAL STRUCTURE OF PROTEASE 3C (C160A MUTANT) FROM SENECA VALLEY TITLE 2 VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDASE C3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEASE 3C; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SENECAVIRUS A; SOURCE 3 ORGANISM_TAXID: 390157; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SENECA VALLEY VIRUS, 3C PROTEASE, PHOSPHOLIPID, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.F.ZHAO,H.ZHANG REVDAT 3 05-JUN-24 8GPH 1 JRNL REVDAT 2 29-NOV-23 8GPH 1 REMARK REVDAT 1 24-MAY-23 8GPH 0 JRNL AUTH H.F.ZHAO,L.MENG,Z.GENG,Z.Q.GAO,Y.H.DONG,H.W.WANG,H.ZHANG JRNL TITL ALLOSTERIC REGULATION OF SENECAVIRUS A 3CPRO PROTEOLYTIC JRNL TITL 2 ACTIVITY BY AN ENDOGENOUS PHOSPHOLIPID. JRNL REF PLOS PATHOG. V. 19 11411 2023 JRNL REFN ESSN 1553-7374 JRNL PMID 37253057 JRNL DOI 10.1371/JOURNAL.PPAT.1011411 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 32104 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) : 0.175 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.260 REMARK 3 FREE R VALUE TEST SET COUNT : 2009 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 27.9790 - 3.8714 1.00 2379 156 0.1583 0.1605 REMARK 3 2 3.8714 - 3.0741 0.99 2237 156 0.1661 0.1795 REMARK 3 3 3.0741 - 2.6858 1.00 2230 148 0.1872 0.1985 REMARK 3 4 2.6858 - 2.4404 1.00 2226 154 0.1902 0.2217 REMARK 3 5 2.4404 - 2.2656 1.00 2213 140 0.1878 0.1945 REMARK 3 6 2.2656 - 2.1321 1.00 2206 149 0.1791 0.2129 REMARK 3 7 2.1321 - 2.0253 0.90 1992 128 0.1704 0.2430 REMARK 3 8 2.0253 - 1.9372 1.00 2188 147 0.1709 0.2092 REMARK 3 9 1.9372 - 1.8626 0.85 1843 136 0.1760 0.1994 REMARK 3 10 1.8626 - 1.7984 1.00 2203 148 0.1784 0.2099 REMARK 3 11 1.7984 - 1.7421 1.00 2183 131 0.1775 0.2077 REMARK 3 12 1.7421 - 1.6923 1.00 2191 146 0.1883 0.2280 REMARK 3 13 1.6923 - 1.6478 0.95 2073 140 0.2090 0.2427 REMARK 3 14 1.6478 - 1.6080 0.88 1931 130 0.2287 0.2477 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 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 1647 REMARK 3 ANGLE : 0.875 2229 REMARK 3 CHIRALITY : 0.056 245 REMARK 3 PLANARITY : 0.006 286 REMARK 3 DIHEDRAL : 11.526 951 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 8GPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031844. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32177 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.608 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.54600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: 6L0T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% (W/V) PEG 8000, 0.1 M HEPES (PH REMARK 280 7.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 23.62650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.85250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.72050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.85250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.62650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.72050 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 1 REMARK 465 PRO A 2 REMARK 465 ASN A 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 177 CA - CB - CG ANGL. DEV. = 14.6 DEGREES 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 GLN A 33 -159.38 -148.86 REMARK 500 VAL A 38 -64.66 -98.80 REMARK 500 TYR A 122 57.89 -142.15 REMARK 500 ARG A 147 70.69 68.46 REMARK 500 VAL A 153 140.03 -171.81 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8GPH A 1 211 UNP A0A1U9IRU2_9PICO DBREF2 8GPH A A0A1U9IRU2 1509 1719 SEQADV 8GPH ALA A 160 UNP A0A1U9IRU CYS 1668 ENGINEERED MUTATION SEQRES 1 A 211 GLN PRO ASN VAL ASP MET GLY PHE GLU ALA ALA VAL ALA SEQRES 2 A 211 LYS LYS VAL VAL VAL PRO ILE THR PHE MET VAL PRO ASN SEQRES 3 A 211 ARG PRO SER GLY LEU THR GLN SER ALA LEU LEU VAL THR SEQRES 4 A 211 GLY ARG THR PHE LEU ILE ASN GLU HIS THR TRP SER ASN SEQRES 5 A 211 PRO SER TRP THR SER PHE THR ILE ARG GLY GLU VAL HIS SEQRES 6 A 211 THR ARG ASP GLU PRO PHE GLN THR VAL HIS PHE THR HIS SEQRES 7 A 211 HIS GLY ILE PRO THR ASP LEU MET MET VAL ARG LEU GLY SEQRES 8 A 211 PRO GLY ASN SER PHE PRO ASN ASN LEU ASP LYS PHE GLY SEQRES 9 A 211 LEU ASP GLN MET PRO ALA ARG ASN SER ARG VAL VAL GLY SEQRES 10 A 211 VAL SER SER SER TYR GLY ASN PHE PHE PHE SER GLY ASN SEQRES 11 A 211 PHE LEU GLY PHE VAL ASP SER ILE THR SER GLU GLN GLY SEQRES 12 A 211 THR TYR ALA ARG LEU PHE ARG TYR ARG VAL THR THR TYR SEQRES 13 A 211 LYS GLY TRP ALA GLY SER ALA LEU VAL CYS GLU ALA GLY SEQRES 14 A 211 GLY VAL ARG ARG ILE ILE GLY LEU HIS SER ALA GLY ALA SEQRES 15 A 211 ALA GLY ILE GLY ALA GLY THR TYR ILE SER LYS LEU GLY SEQRES 16 A 211 LEU ILE LYS ALA LEU LYS HIS LEU GLY GLU PRO LEU ALA SEQRES 17 A 211 THR MET GLN HET PEG A 301 7 HET GOL A 302 6 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PEG C4 H10 O3 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *210(H2 O) HELIX 1 AA1 MET A 6 VAL A 16 1 11 HELIX 2 AA2 GLU A 47 ASN A 52 1 6 HELIX 3 AA3 ASN A 99 PHE A 103 5 5 HELIX 4 AA4 SER A 192 LEU A 203 1 12 SHEET 1 AA1 7 GLU A 63 THR A 66 0 SHEET 2 AA1 7 SER A 57 ILE A 60 -1 N PHE A 58 O HIS A 65 SHEET 3 AA1 7 VAL A 17 MET A 23 -1 N MET A 23 O SER A 57 SHEET 4 AA1 7 LEU A 31 THR A 39 -1 O LEU A 31 N PHE A 22 SHEET 5 AA1 7 THR A 42 ASN A 46 -1 O THR A 42 N THR A 39 SHEET 6 AA1 7 ILE A 81 ARG A 89 -1 O VAL A 88 N PHE A 43 SHEET 7 AA1 7 GLN A 72 HIS A 78 -1 N GLN A 72 O ARG A 89 SHEET 1 AA2 7 ARG A 114 SER A 119 0 SHEET 2 AA2 7 PHE A 125 SER A 140 -1 O PHE A 127 N GLY A 117 SHEET 3 AA2 7 GLY A 143 ARG A 152 -1 O ARG A 150 N LEU A 132 SHEET 4 AA2 7 ILE A 185 TYR A 190 -1 O GLY A 188 N PHE A 149 SHEET 5 AA2 7 VAL A 171 ALA A 182 -1 N SER A 179 O ALA A 187 SHEET 6 AA2 7 ALA A 163 ALA A 168 -1 N LEU A 164 O ILE A 175 SHEET 7 AA2 7 ARG A 114 SER A 119 -1 N VAL A 116 O VAL A 165 CRYST1 47.253 69.441 75.705 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 0.021163 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013209 0.00000