HEADER HYDROLASE 31-AUG-19 6KU7 TITLE STRUCTURE OF HRV-C 3C PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; 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: RHINOVIRUS C; SOURCE 3 ORGANISM_TAXID: 463676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS HRV, 3C, PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHU,S.YUAN REVDAT 3 22-NOV-23 6KU7 1 REMARK REVDAT 2 16-SEP-20 6KU7 1 JRNL REVDAT 1 25-MAR-20 6KU7 0 JRNL AUTH S.YUAN,K.FAN,Z.CHEN,Y.SUN,H.HOU,L.ZHU JRNL TITL STRUCTURE OF THE HRV-C 3C-RUPINTRIVIR COMPLEX PROVIDES NEW JRNL TITL 2 INSIGHTS FOR INHIBITOR DESIGN. JRNL REF VIROL SIN V. 35 445 2020 JRNL REFN ISSN 1995-820X JRNL PMID 32103448 JRNL DOI 10.1007/S12250-020-00196-4 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.11 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 13546 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 670 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 2.3200 - 2.1500 0.00 0 0 0.2466 0.3029 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6KU7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 293.15 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) : 0.998 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13578 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 V1.11 REMARK 200 STARTING MODEL: 3ZV8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CITRIC ACID, 0.05 M BIS-TRIS REMARK 280 PROPANE, PH 5.0, 16% (W/V) POLYETHYLENE GLYCOL 3,350., BATCH REMARK 280 MODE, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 49.05050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.05050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.04700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.36900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.04700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.36900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.05050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.04700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.36900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.05050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.04700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.36900 REMARK 290 SMTRY3 8 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 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 O HOH A 274 O HOH A 281 1.98 REMARK 500 OH TYR A 138 ND1 HIS A 161 2.05 REMARK 500 O HOH A 283 O HOH A 284 2.09 REMARK 500 NH2 ARG A 8 O HOH A 201 2.10 REMARK 500 OE1 GLN A 94 O HOH A 202 2.13 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 CD ARG A 95 NH1 ARG A 95 4555 1.87 REMARK 500 NE ARG A 95 NH1 ARG A 95 4555 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 95 CG - CD - NE ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 95 NE - CZ - NH2 ANGL. DEV. = 6.5 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 ASP A 32 -126.07 52.59 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6KU7 A 1 180 UNP A0A219Y1F5_9ENTO DBREF2 6KU7 A A0A219Y1F5 1511 1690 SEQADV 6KU7 HIS A -5 UNP A0A219Y1F EXPRESSION TAG SEQADV 6KU7 HIS A -4 UNP A0A219Y1F EXPRESSION TAG SEQADV 6KU7 HIS A -3 UNP A0A219Y1F EXPRESSION TAG SEQADV 6KU7 HIS A -2 UNP A0A219Y1F EXPRESSION TAG SEQADV 6KU7 HIS A -1 UNP A0A219Y1F EXPRESSION TAG SEQADV 6KU7 HIS A 0 UNP A0A219Y1F EXPRESSION TAG SEQRES 1 A 186 HIS HIS HIS HIS HIS HIS GLY PRO GLU HIS GLU PHE VAL SEQRES 2 A 186 ARG ALA LEU ILE LYS ARG ASN CYS HIS VAL ILE THR THR SEQRES 3 A 186 SER LYS GLY GLU PHE ASN MET LEU GLY ILE HIS ASP ASN SEQRES 4 A 186 CYS ALA VAL VAL PRO THR HIS ALA GLU CYS GLY ASP SER SEQRES 5 A 186 VAL THR ILE ASP GLY ARG GLU VAL ARG VAL LEU LYS GLN SEQRES 6 A 186 CYS ILE LEU THR ASP THR ASN ASP THR ASP THR GLU ILE SEQRES 7 A 186 THR LEU LEU TRP LEU ASP GLN ASN GLU LYS PHE ARG ASP SEQRES 8 A 186 ILE ARG ARG PHE ILE PRO GLU HIS GLN ARG GLU TRP SER SEQRES 9 A 186 ASN MET HIS LEU ALA THR ASN VAL THR LYS PHE PRO MET SEQRES 10 A 186 LEU ASP VAL GLU VAL GLY THR VAL ILE PRO TYR GLY GLU SEQRES 11 A 186 VAL ASN LEU SER GLY ASN PRO THR CYS ARG LEU LEU LYS SEQRES 12 A 186 TYR ASN TYR PRO THR LYS PRO GLY GLN CYS GLY GLY VAL SEQRES 13 A 186 ILE ALA ASN THR GLY ASN ILE VAL ALA ILE HIS VAL GLY SEQRES 14 A 186 GLY ASN GLY ARG VAL GLY TYR GLY ALA ALA LEU LEU ARG SEQRES 15 A 186 LYS TYR PHE ALA FORMUL 2 HOH *86(H2 O) HELIX 1 AA1 GLY A 1 ASN A 14 1 14 HELIX 2 AA2 HIS A 40 GLU A 42 5 3 HELIX 3 AA3 ILE A 86 ILE A 90 5 5 HELIX 4 AA4 LYS A 143 CYS A 147 5 5 HELIX 5 AA5 LEU A 175 PHE A 179 5 5 SHEET 1 AA1 7 CYS A 15 THR A 20 0 SHEET 2 AA1 7 GLY A 23 HIS A 31 -1 O PHE A 25 N ILE A 18 SHEET 3 AA1 7 CYS A 34 PRO A 38 -1 O CYS A 34 N HIS A 31 SHEET 4 AA1 7 ASP A 69 LEU A 77 -1 O LEU A 75 N ALA A 35 SHEET 5 AA1 7 ARG A 52 THR A 63 -1 N LYS A 58 O TRP A 76 SHEET 6 AA1 7 SER A 46 ILE A 49 -1 N ILE A 49 O ARG A 52 SHEET 7 AA1 7 CYS A 15 THR A 20 -1 N THR A 19 O THR A 48 SHEET 1 AA2 7 TRP A 97 THR A 104 0 SHEET 2 AA2 7 LEU A 112 LEU A 127 -1 O VAL A 114 N LEU A 102 SHEET 3 AA2 7 ASN A 130 TYR A 138 -1 O LEU A 135 N TYR A 122 SHEET 4 AA2 7 GLY A 169 ALA A 173 -1 O GLY A 171 N LEU A 136 SHEET 5 AA2 7 ASN A 156 GLY A 164 -1 N VAL A 162 O TYR A 170 SHEET 6 AA2 7 VAL A 150 ASN A 153 -1 N ILE A 151 O ALA A 159 SHEET 7 AA2 7 TRP A 97 THR A 104 -1 N ALA A 103 O VAL A 150 CRYST1 52.094 94.738 98.101 90.00 90.00 90.00 C 2 2 21 8 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 0.019196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010194 0.00000