HEADER VIRAL PROTEIN 25-AUG-22 8GOT TITLE CRYSTAL STRUCTURE OF WILD-TYPE PROTEASE 3C FROM SENECA VALLEY 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 8GOT 1 JRNL REVDAT 2 29-NOV-23 8GOT 1 REMARK REVDAT 1 24-MAY-23 8GOT 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. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.640 REMARK 3 FREE R VALUE TEST SET COUNT : 820 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 40.0860 - 3.6144 1.00 2948 157 0.1838 0.2099 REMARK 3 2 3.6144 - 2.8691 1.00 2822 134 0.2193 0.2639 REMARK 3 3 2.8691 - 2.5065 1.00 2757 170 0.2577 0.3359 REMARK 3 4 2.5065 - 2.2773 1.00 2798 109 0.2492 0.3041 REMARK 3 5 2.2773 - 2.1141 1.00 2773 122 0.2550 0.3056 REMARK 3 6 2.1141 - 1.9895 1.00 2740 128 0.2731 0.3305 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 44.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.61 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 1747 REMARK 3 ANGLE : 0.919 2345 REMARK 3 CHIRALITY : 0.058 248 REMARK 3 PLANARITY : 0.005 297 REMARK 3 DIHEDRAL : 15.147 1024 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 8GOT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031840. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-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 : BL18U1 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25880 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.989 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 35.90 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 20.80 REMARK 200 R MERGE FOR SHELL (I) : 0.75200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350, 1% (W/V) TRYPTONE, REMARK 280 0.05% (W/V) SODIUM AZIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 23.65150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.75200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.74800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.75200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.65150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.74800 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: 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 VAL A 38 -62.38 -96.91 REMARK 500 ARG A 147 72.08 64.56 REMARK 500 VAL A 153 142.09 -173.06 REMARK 500 ALA A 182 101.11 -164.46 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8GOT A 1 211 UNP A0A1U9IRU2_9PICO DBREF2 8GOT A A0A1U9IRU2 1509 1719 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 CYS 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 K8U A 301 102 HET GOL A 302 6 HETNAM K8U [(2~{S})-2-HEXADECANOYLOXY-3-[[(2~{R})-3-[[(2~{S})-3- HETNAM 2 K8U [(5~{E},8~{E},11~{Z},14~{E})-ICOSA-5,8,11,14- HETNAM 3 K8U TETRAENOYL]OXY-2-[(9~{E},12~{Z})-OCTADECA-9,12- HETNAM 4 K8U DIENOYL]OXY-PROPOXY]-OXIDANYL-PHOSPHORYL]OXY-2- HETNAM 5 K8U OXIDANYL-PROPOXY]-OXIDANYL-PHOSPHORYL]OXY-PROPYL] HETNAM 6 K8U ICOSANOATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 K8U C83 H150 O17 P2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *49(H2 O) HELIX 1 AA1 MET A 6 VAL A 16 1 11 HELIX 2 AA2 GLU A 47 SER A 51 1 5 HELIX 3 AA3 ASN A 99 PHE A 103 5 5 HELIX 4 AA4 SER A 192 GLY A 204 1 13 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 VAL A 74 O MET A 87 SHEET 1 AA2 7 ARG A 114 SER A 119 0 SHEET 2 AA2 7 PHE A 125 SER A 140 -1 O GLY A 129 N VAL A 115 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 GLY A 181 -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 GLY A 176 SHEET 7 AA2 7 ARG A 114 SER A 119 -1 N VAL A 116 O VAL A 165 CRYST1 47.303 69.496 75.504 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 0.021140 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014389 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013244 0.00000