HEADER VIRAL PROTEIN 27-JAN-24 8Y2T TITLE CRYSTAL STRUCTURE OF 3C PROTEASE FROM COXSACKIEVIRUS B3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE 3C; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COXSACKIEVIRUS B3; SOURCE 3 ORGANISM_TAXID: 12072; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COXSACKIEVIRUS B3, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.H.JIANG,X.F.ZOU,J.ZHANG,J.LI REVDAT 1 14-AUG-24 8Y2T 0 JRNL AUTH H.JIANG,C.LIN,J.CHANG,X.ZOU,J.ZHANG,J.LI JRNL TITL CRYSTAL STRUCTURES OF THE 3C PROTEASES FROM COXSACKIEVIRUS JRNL TITL 2 B3 AND B4. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 80 183 2024 JRNL REFN ESSN 2053-230X JRNL PMID 39052022 JRNL DOI 10.1107/S2053230X24006915 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.382 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 9498 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.854 REMARK 3 FREE R VALUE TEST SET COUNT : 461 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 33.7519 - 3.0267 0.96 3261 158 0.1774 0.2086 REMARK 3 2 3.0267 - 2.4026 0.88 2936 143 0.2800 0.3536 REMARK 3 3 2.4026 - 2.1000 0.86 2840 160 0.2503 0.3426 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) : 0.245 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.52 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.96 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 : 0.008 1426 REMARK 3 ANGLE : 1.033 1924 REMARK 3 CHIRALITY : 0.060 211 REMARK 3 PLANARITY : 0.005 250 REMARK 3 DIHEDRAL : 7.209 848 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 8Y2T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 31-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1300044540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-23 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 : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9502 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M BIS-TRIS PH 6.5, 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 39.11200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.28650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.11200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.28650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 60 CD CE NZ REMARK 480 LYS A 65 CD CE NZ REMARK 480 LYS A 108 CB CG CD CE NZ REMARK 480 ARG A 143 NE REMARK 480 ALA A 147 N CA C O 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 NZ LYS A 133 O HOH A 201 2.10 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 32 -115.47 57.32 REMARK 500 LYS A 42 58.23 37.67 REMARK 500 GLU A 71 31.46 72.10 REMARK 500 PRO A 141 82.04 -52.60 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8Y2T A 1 180 UNP A0A2H4Z5X4_9ENTO DBREF2 8Y2T A A0A2H4Z5X4 1541 1720 SEQADV 8Y2T ALA A 147 UNP A0A2H4Z5X CYS 1687 CONFLICT SEQRES 1 A 180 GLY PRO ALA PHE GLU PHE ALA VAL ALA MET MET LYS ARG SEQRES 2 A 180 ASN SER SER THR VAL LYS THR GLU TYR GLY GLU PHE THR SEQRES 3 A 180 MET LEU GLY ILE TYR ASP ARG TRP ALA VAL LEU PRO ARG SEQRES 4 A 180 HIS ALA LYS PRO GLY PRO THR ILE LEU MET ASN ASP GLN SEQRES 5 A 180 GLU VAL GLY VAL LEU ASP ALA LYS GLU LEU VAL ASP LYS SEQRES 6 A 180 ASP GLY THR ASN LEU GLU LEU THR LEU LEU LYS LEU ASN SEQRES 7 A 180 ARG ASN GLU LYS PHE ARG ASP ILE ARG GLY PHE LEU ALA SEQRES 8 A 180 LYS GLU GLU VAL GLU VAL ASN GLU ALA VAL LEU ALA ILE SEQRES 9 A 180 ASN THR SER LYS PHE PRO ASN MET TYR ILE PRO VAL GLY SEQRES 10 A 180 GLN VAL THR GLU TYR GLY PHE LEU ASN LEU GLY GLY THR SEQRES 11 A 180 PRO THR LYS ARG MET LEU MET TYR ASN PHE PRO THR ARG SEQRES 12 A 180 ALA GLY GLN ALA GLY GLY VAL LEU MET SER THR GLY LYS SEQRES 13 A 180 VAL LEU GLY ILE HIS VAL GLY GLY ASN GLY HIS GLN GLY SEQRES 14 A 180 PHE SER ALA ALA LEU LEU LYS HIS TYR PHE ASN FORMUL 2 HOH *17(H2 O) HELIX 1 AA1 GLY A 1 ASN A 14 1 14 HELIX 2 AA2 HIS A 40 LYS A 42 5 3 HELIX 3 AA3 ILE A 86 LEU A 90 5 5 HELIX 4 AA4 LEU A 175 ASN A 180 5 6 SHEET 1 AA1 7 SER A 15 THR A 20 0 SHEET 2 AA1 7 GLY A 23 TYR A 31 -1 O PHE A 25 N VAL A 18 SHEET 3 AA1 7 TRP A 34 PRO A 38 -1 O TRP A 34 N TYR A 31 SHEET 4 AA1 7 ASN A 69 LEU A 77 -1 O THR A 73 N LEU A 37 SHEET 5 AA1 7 GLN A 52 VAL A 63 -1 N LEU A 62 O LEU A 72 SHEET 6 AA1 7 THR A 46 MET A 49 -1 N MET A 49 O GLN A 52 SHEET 7 AA1 7 SER A 15 THR A 20 -1 N LYS A 19 O LEU A 48 SHEET 1 AA2 7 VAL A 97 ILE A 104 0 SHEET 2 AA2 7 MET A 112 LEU A 127 -1 O ILE A 114 N LEU A 102 SHEET 3 AA2 7 THR A 130 ASN A 139 -1 O THR A 130 N LEU A 127 SHEET 4 AA2 7 GLN A 168 ALA A 173 -1 O SER A 171 N LEU A 136 SHEET 5 AA2 7 LYS A 156 GLY A 164 -1 N VAL A 162 O PHE A 170 SHEET 6 AA2 7 VAL A 150 SER A 153 -1 N LEU A 151 O GLY A 159 SHEET 7 AA2 7 VAL A 97 ILE A 104 -1 N VAL A 101 O MET A 152 CRYST1 78.224 64.573 39.743 90.00 115.27 90.00 C 1 2 1 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 0.012784 0.000000 0.006034 0.00000 SCALE2 0.000000 0.015486 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027824 0.00000