PDB Short entry for 7MHQ HEADER HYDROLASE 15-APR-21 7MHQ TITLE ENSEMBLE REFINEMENT STRUCTURE OF SARS-COV-2 MAIN PROTEASE (MPRO) AT TITLE 2 310 K COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS SARS-COV-2, CORONAVIRUS, MAIN PROTEASE, 3CLPRO, MPRO, HYDROLASE, KEYWDS 2 ENSEMBLE REFINEMENT, TEMPERATURE SERIES, TEMPERATURE, KEYWDS 3 MULTITEMPERATURE EXPDTA X-RAY DIFFRACTION NUMMDL 36 AUTHOR A.EBRAHIM,B.T.RILEY,D.KUMARAN,B.ANDI,M.R.FUCHS,S.MCSWEENEY,D.A.KEEDY REVDAT 5 18-OCT-23 7MHQ 1 REMARK REVDAT 4 07-SEP-22 7MHQ 1 JRNL REVDAT 3 06-APR-22 7MHQ 1 TITLE COMPND SOURCE KEYWDS REVDAT 3 2 1 JRNL REMARK HET HETNAM REVDAT 3 3 1 FORMUL HELIX SHEET LINK REVDAT 3 4 1 SITE ATOM REVDAT 2 26-MAY-21 7MHQ 1 JRNL REVDAT 1 12-MAY-21 7MHQ 0 JRNL AUTH A.EBRAHIM,B.T.RILEY,D.KUMARAN,B.ANDI,M.R.FUCHS,S.MCSWEENEY, JRNL AUTH 2 D.A.KEEDY JRNL TITL THE TEMPERATURE-DEPENDENT CONFORMATIONAL ENSEMBLE OF JRNL TITL 2 SARS-COV-2 MAIN PROTEASE (M PRO ) JRNL REF IUCRJ V. 9 682 2022 JRNL REFN ESSN 2052-2525 JRNL DOI 10.1107/S2052252522007497 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.ENSEMBLE_REFINEMENT:1.19.2_4158) 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 19426 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 : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 43.9676 - 3.5600 0.99 3162 148 0.1357 0.1870 REMARK 3 2 3.5600 - 2.8300 1.00 3104 136 0.1609 0.2229 REMARK 3 3 2.8300 - 2.4700 1.00 3094 158 0.1952 0.2899 REMARK 3 4 2.4700 - 2.2400 1.00 3056 161 0.2278 0.3135 REMARK 3 5 2.2400 - 2.0800 1.00 3089 145 0.2630 0.3216 REMARK 3 6 2.0800 - 1.9601 1.00 3043 130 0.3286 0.4296 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 12.6272 0.9329 4.7913 REMARK 3 T TENSOR REMARK 3 T11: 0.4637 T22: 0.4917 REMARK 3 T33: 0.4961 T12: 0.0055 REMARK 3 T13: 0.0088 T23: -0.0236 REMARK 3 L TENSOR REMARK 3 L11: 0.5979 L22: 0.5802 REMARK 3 L33: 0.9464 L12: -0.0258 REMARK 3 L13: 0.1256 L23: -0.1562 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: -0.0256 S13: -0.0269 REMARK 3 S21: 0.0178 S22: -0.0147 S23: -0.0379 REMARK 3 S31: 0.0212 S32: 0.0282 S33: 0.0145 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 7MHQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000255384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 310 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 0.7.32-G2F242514-DIALS-3.0 REMARK 200 DATA SCALING SOFTWARE : DIALS 3.0.0-GB83E1FCE8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19444 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 43.968 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.590 REMARK 200 R MERGE (I) : 0.19520 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.3964 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.71 REMARK 200 R MERGE FOR SHELL (I) : 1.80450 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.322 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.18.2_3874 REMARK 200 STARTING MODEL: 6YB7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 4000, 100 MM HEPES PH 7.0, 3- REMARK 280 -5% DMSO, VAPOR DIFFUSION, SITTING 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 57.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.15000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.14500 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: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 615 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 621 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 CYS A 300 CB CYS A 300 SG 0.192 REMARK 500 2 CYS A 156 CB CYS A 156 SG -0.103 REMARK 500 2 TRP A 218 CB TRP A 218 CG 0.137 REMARK 500 3 CYS A 117 CB CYS A 117 SG -0.098 REMARK 500 3 CYS A 145 CB CYS A 145 SG 0.124 REMARK 500 3 CYS A 156 CB CYS A 156 SG 0.117 REMARK 500 3 TRP A 218 CB TRP A 218 CG 0.149 REMARK 500 4 ILE A 106 C GLN A 107 N -0.169 REMARK 500 4 CYS A 145 CB CYS A 145 SG 0.200 REMARK 500 6 CYS A 156 CB CYS A 156 SG -0.101 REMARK 500 6 CYS A 300 CB CYS A 300 SG 0.175 REMARK 500 7 CYS A 117 CB CYS A 117 SG -0.097 REMARK 500 7 CYS A 300 CB CYS A 300 SG 0.124 REMARK 500 8 CYS A 145 CB CYS A 145 SG 0.203 REMARK 500 8 CYS A 265 CB CYS A 265 SG -0.101 REMARK 500 8 CYS A 300 CB CYS A 300 SG 0.198 REMARK 500 9 CYS A 145 CB CYS A 145 SG 0.213 REMARK 500 9 CYS A 265 CB CYS A 265 SG -0.099 REMARK 500 10 ILE A 106 C GLN A 107 N -0.206 REMARK 500 10 CYS A 145 CB CYS A 145 SG 0.232 REMARK 500 11 CYS A 44 CB CYS A 44 SG -0.112 REMARK 500 11 CYS A 265 CB CYS A 265 SG -0.105 REMARK 500 13 CYS A 145 CB CYS A 145 SG 0.137 REMARK 500 13 TRP A 218 CB TRP A 218 CG 0.120 REMARK 500 14 CYS A 145 CB CYS A 145 SG 0.128 REMARK 500 14 TRP A 218 CB TRP A 218 CG 0.121 REMARK 500 14 VAL A 303 CB VAL A 303 CG2 -0.149 REMARK 500 15 ILE A 106 C GLN A 107 N -0.227 REMARK 500 16 GLU A 55 CB GLU A 55 CG 0.133 REMARK 500 17 ILE A 152 CB ILE A 152 CG2 -0.199 REMARK 500 18 GLU A 47 CG GLU A 47 CD 0.096 REMARK 500 18 CYS A 145 CB CYS A 145 SG -0.220 REMARK 500 18 CYS A 300 CB CYS A 300 SG 0.203 REMARK 500 19 CYS A 145 CB CYS A 145 SG 0.175 REMARK 500 19 TRP A 218 CB TRP A 218 CG 0.130 REMARK 500 20 CYS A 117 CB CYS A 117 SG -0.101 REMARK 500 20 CYS A 128 CB CYS A 128 SG -0.117 REMARK 500 21 CYS A 128 CB CYS A 128 SG -0.279 REMARK 500 22 CYS A 22 CB CYS A 22 SG 0.149 REMARK 500 22 CYS A 44 CB CYS A 44 SG -0.111 REMARK 500 22 ILE A 106 C GLN A 107 N -0.182 REMARK 500 22 CYS A 156 CB CYS A 156 SG -0.120 REMARK 500 23 TRP A 218 CB TRP A 218 CG 0.123 REMARK 500 25 CYS A 22 CB CYS A 22 SG 0.117 REMARK 500 25 MET A 130 CG MET A 130 SD -0.169 REMARK 500 25 CYS A 145 CB CYS A 145 SG 0.105 REMARK 500 26 CYS A 300 CB CYS A 300 SG -0.108 REMARK 500 27 GLU A 270 CB GLU A 270 CG 0.120 REMARK 500 27 GLU A 270 CG GLU A 270 CD 0.099 REMARK 500 29 CYS A 145 CB CYS A 145 SG 0.134 REMARK 500 REMARK 500 THIS ENTRY HAS 60 BOND DEVIATIONS. 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 1 CYS A 22 CA - CB - SG ANGL. DEV. = -13.7 DEGREES REMARK 500 2 ASP A 216 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 6 CYS A 300 CA - CB - SG ANGL. DEV. = 9.2 DEGREES REMARK 500 9 MET A 49 CA - CB - CG ANGL. DEV. = 12.3 DEGREES REMARK 500 9 MET A 130 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 9 CYS A 145 CA - CB - SG ANGL. DEV. = 10.8 DEGREES REMARK 500 9 CYS A 300 CA - CB - SG ANGL. DEV. = -11.7 DEGREES REMARK 500 10 CYS A 145 CA - CB - SG ANGL. DEV. = 12.7 DEGREES REMARK 500 10 TRP A 218 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 12 LEU A 67 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 14 GLU A 47 CA - CB - CG ANGL. DEV. = 13.5 DEGREES REMARK 500 16 LEU A 271 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 18 GLY A 275 N - CA - C ANGL. DEV. = 15.4 DEGREES REMARK 500 20 LEU A 27 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 20 CYS A 44 CA - CB - SG ANGL. DEV. = -13.4 DEGREES REMARK 500 20 CYS A 128 CA - CB - SG ANGL. DEV. = -24.8 DEGREES REMARK 500 20 TYR A 154 CA - CB - CG ANGL. DEV. = 12.4 DEGREES REMARK 500 20 TYR A 154 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ASP A 155 CB - CG - OD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 25 CYS A 22 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 25 MET A 82 CA - CB - CG ANGL. DEV. = 11.3 DEGREES REMARK 500 25 MET A 130 CB - CG - SD ANGL. DEV. = -19.9 DEGREES REMARK 500 25 CYS A 145 CA - CB - SG ANGL. DEV. = 9.6 DEGREES REMARK 500 25 LEU A 271 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 26 CYS A 300 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 27 LEU A 286 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 27 CYS A 300 CA - CB - SG ANGL. DEV. = -14.1 DEGREES REMARK 500 28 TYR A 154 CA - CB - CG ANGL. DEV. = 12.8 DEGREES REMARK 500 29 CYS A 145 CA - CB - SG ANGL. DEV. = 10.9 DEGREES REMARK 500 31 LEU A 242 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 32 LEU A 50 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 35 MET A 6 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 35 LEU A 67 CA - CB - CG ANGL. DEV. = 17.1 DEGREES REMARK 500 35 LEU A 75 CA - CB - CG ANGL. DEV. = -15.6 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 1 CYS A 22 -130.55 -68.34 REMARK 500 1 THR A 24 -160.87 -107.19 REMARK 500 1 THR A 25 108.91 60.41 REMARK 500 1 ASP A 33 -131.77 38.47 REMARK 500 1 ASP A 34 44.06 -104.78 REMARK 500 1 GLU A 47 21.64 20.39 REMARK 500 1 ASP A 48 -174.26 62.08 REMARK 500 1 MET A 49 41.10 -97.49 REMARK 500 1 ASN A 51 67.60 161.02 REMARK 500 1 ASN A 72 94.74 166.95 REMARK 500 1 VAL A 73 -118.06 172.56 REMARK 500 1 GLN A 74 -56.90 -144.92 REMARK 500 1 LEU A 75 120.48 60.60 REMARK 500 1 ASN A 84 -120.76 28.94 REMARK 500 1 PRO A 99 -166.76 -113.89 REMARK 500 1 PRO A 108 154.18 -46.96 REMARK 500 1 ASN A 119 55.52 27.97 REMARK 500 1 ASP A 153 -52.66 -137.28 REMARK 500 1 TYR A 154 -127.09 -86.44 REMARK 500 1 ASP A 155 39.25 -95.99 REMARK 500 1 SER A 158 78.99 -108.09 REMARK 500 1 THR A 169 56.05 -108.28 REMARK 500 1 ALA A 193 156.43 -42.18 REMARK 500 1 ALA A 194 114.43 -169.80 REMARK 500 1 ASN A 214 35.44 -91.21 REMARK 500 1 TRP A 218 24.06 -150.95 REMARK 500 1 ASN A 238 36.80 77.52 REMARK 500 1 THR A 243 -153.36 -122.87 REMARK 500 1 GLN A 273 -134.95 -63.86 REMARK 500 1 ASN A 274 82.29 -53.14 REMARK 500 1 MET A 276 92.18 79.86 REMARK 500 1 ASN A 277 142.37 115.07 REMARK 500 1 ARG A 279 -152.34 -75.40 REMARK 500 1 SER A 301 171.00 102.80 REMARK 500 1 VAL A 303 160.04 -31.69 REMARK 500 1 PHE A 305 -78.60 168.98 REMARK 500 2 CYS A 22 -127.98 -87.65 REMARK 500 2 THR A 24 -78.12 -105.68 REMARK 500 2 THR A 25 133.01 -31.41 REMARK 500 2 ASP A 33 -132.02 45.65 REMARK 500 2 ASP A 34 65.94 -112.14 REMARK 500 2 GLU A 47 25.79 40.23 REMARK 500 2 ASP A 48 -171.68 30.97 REMARK 500 2 MET A 49 19.01 -59.85 REMARK 500 2 SER A 62 -170.81 170.28 REMARK 500 2 ASN A 72 99.52 110.75 REMARK 500 2 VAL A 73 119.64 132.36 REMARK 500 2 LEU A 75 152.41 53.91 REMARK 500 2 HIS A 80 136.76 -170.45 REMARK 500 2 ASN A 84 -124.61 55.02 REMARK 500 REMARK 500 THIS ENTRY HAS 1175 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 64 ASN A 65 1 146.20 REMARK 500 GLN A 74 LEU A 75 1 -144.64 REMARK 500 TYR A 154 ASP A 155 1 147.98 REMARK 500 ARG A 279 THR A 280 1 -145.85 REMARK 500 CYS A 44 THR A 45 2 135.97 REMARK 500 HIS A 64 ASN A 65 2 146.56 REMARK 500 ILE A 152 ASP A 153 2 143.42 REMARK 500 LYS A 236 TYR A 237 2 149.39 REMARK 500 CYS A 300 SER A 301 2 148.98 REMARK 500 VAL A 303 THR A 304 2 -147.71 REMARK 500 PRO A 99 LYS A 100 3 144.17 REMARK 500 GLN A 110 THR A 111 3 -147.07 REMARK 500 GLY A 278 ARG A 279 3 -142.39 REMARK 500 SER A 301 GLY A 302 3 144.96 REMARK 500 VAL A 303 THR A 304 3 -148.10 REMARK 500 THR A 24 THR A 25 4 -146.90 REMARK 500 ASP A 48 MET A 49 4 145.79 REMARK 500 GLN A 189 THR A 190 4 140.91 REMARK 500 GLN A 273 ASN A 274 4 144.31 REMARK 500 CYS A 300 SER A 301 4 -124.29 REMARK 500 VAL A 303 THR A 304 4 -143.24 REMARK 500 CYS A 44 THR A 45 5 129.68 REMARK 500 THR A 45 SER A 46 5 -148.65 REMARK 500 GLU A 47 ASP A 48 5 -131.06 REMARK 500 VAL A 73 GLN A 74 5 -149.61 REMARK 500 MET A 276 ASN A 277 5 128.17 REMARK 500 CYS A 300 SER A 301 5 -96.76 REMARK 500 SER A 301 GLY A 302 5 -144.79 REMARK 500 VAL A 303 THR A 304 5 -136.04 REMARK 500 THR A 304 PHE A 305 5 -133.50 REMARK 500 CYS A 44 THR A 45 6 113.42 REMARK 500 THR A 45 SER A 46 6 146.23 REMARK 500 TYR A 154 ASP A 155 6 148.84 REMARK 500 GLU A 178 GLY A 179 6 148.51 REMARK 500 GLY A 275 MET A 276 6 136.84 REMARK 500 ASN A 277 GLY A 278 6 136.88 REMARK 500 ARG A 279 THR A 280 6 -148.99 REMARK 500 GLY A 302 VAL A 303 6 -148.79 REMARK 500 CYS A 44 THR A 45 7 111.77 REMARK 500 VAL A 73 GLN A 74 7 -132.41 REMARK 500 LEU A 75 ARG A 76 7 -145.02 REMARK 500 ARG A 76 VAL A 77 7 -146.12 REMARK 500 TYR A 154 ASP A 155 7 122.06 REMARK 500 MET A 276 ASN A 277 7 124.89 REMARK 500 CYS A 300 SER A 301 7 -108.84 REMARK 500 ILE A 152 ASP A 153 8 -147.05 REMARK 500 ARG A 298 GLN A 299 8 -130.20 REMARK 500 GLN A 299 CYS A 300 8 -109.87 REMARK 500 CYS A 300 SER A 301 8 -127.96 REMARK 500 VAL A 303 THR A 304 8 -146.08 REMARK 500 REMARK 500 THIS ENTRY HAS 331 NON CIS, NON-TRANS OMEGA OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 279 0.08 SIDE CHAIN REMARK 500 4 ARG A 298 0.10 SIDE CHAIN REMARK 500 6 ARG A 298 0.08 SIDE CHAIN REMARK 500 7 ARG A 188 0.09 SIDE CHAIN REMARK 500 8 ARG A 222 0.10 SIDE CHAIN REMARK 500 12 ARG A 298 0.09 SIDE CHAIN REMARK 500 13 ARG A 217 0.14 SIDE CHAIN REMARK 500 14 ARG A 279 0.14 SIDE CHAIN REMARK 500 16 ARG A 217 0.09 SIDE CHAIN REMARK 500 17 ARG A 217 0.17 SIDE CHAIN REMARK 500 17 ARG A 279 0.09 SIDE CHAIN REMARK 500 17 ARG A 298 0.11 SIDE CHAIN REMARK 500 18 ARG A 217 0.09 SIDE CHAIN REMARK 500 19 ARG A 279 0.09 SIDE CHAIN REMARK 500 20 ARG A 279 0.10 SIDE CHAIN REMARK 500 20 ARG A 298 0.10 SIDE CHAIN REMARK 500 21 ARG A 217 0.08 SIDE CHAIN REMARK 500 21 ARG A 279 0.11 SIDE CHAIN REMARK 500 21 ARG A 298 0.11 SIDE CHAIN REMARK 500 24 ARG A 105 0.09 SIDE CHAIN REMARK 500 25 ARG A 279 0.09 SIDE CHAIN REMARK 500 26 ARG A 188 0.07 SIDE CHAIN REMARK 500 27 ARG A 222 0.09 SIDE CHAIN REMARK 500 29 ARG A 105 0.09 SIDE CHAIN REMARK 500 31 ARG A 60 0.10 SIDE CHAIN REMARK 500 32 ARG A 217 0.09 SIDE CHAIN REMARK 500 34 ARG A 217 0.15 SIDE CHAIN REMARK 500 34 ARG A 298 0.10 SIDE CHAIN REMARK 500 36 ARG A 217 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 606 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A 616 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH A 608 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 602 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 633 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH A 626 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH A 629 DISTANCE = 5.97 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 NE2 REMARK 620 2 CYS A 145 SG 104.6 REMARK 620 3 HOH A 642 O 51.5 53.4 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7MHL RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 100 K REMARK 900 RELATED ID: 7MHM RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 240 K REMARK 900 RELATED ID: 7MHN RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 277 K REMARK 900 RELATED ID: 7MHO RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 298 K REMARK 900 RELATED ID: 7MHP RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 298 K, 99% RH REMARK 900 RELATED ID: 7MHF RELATED DB: PDB REMARK 900 REFINEMENT AT 100 K REMARK 900 RELATED ID: 7MHG RELATED DB: PDB REMARK 900 REFINEMENT AT 240 K REMARK 900 RELATED ID: 7MHH RELATED DB: PDB REMARK 900 REFINEMENT AT 277 K REMARK 900 RELATED ID: 7MHI RELATED DB: PDB REMARK 900 REFINEMENT AT 298 K REMARK 900 RELATED ID: 7MHJ RELATED DB: PDB REMARK 900 REFINEMENT AT 298 K, 99% RH REMARK 900 RELATED ID: 7MHK RELATED DB: PDB REMARK 900 REFINEMENT AT 310 K DBREF 7MHQ A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN HET DMS A 501 10 HET DMS A 502 10 HET ZN A 503 1 HETNAM DMS DIMETHYL SULFOXIDE HETNAM ZN ZINC ION FORMUL 2 DMS 2(C2 H6 O S) FORMUL 4 ZN ZN 2+ FORMUL 5 HOH *45(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 ASN A 53 LEU A 58 1 6 HELIX 4 AA4 SER A 62 PHE A 66 5 5 HELIX 5 AA5 ILE A 200 ASN A 214 1 15 HELIX 6 AA6 THR A 226 TYR A 237 1 12 HELIX 7 AA7 THR A 243 LEU A 250 1 8 HELIX 8 AA8 LEU A 250 GLY A 258 1 9 HELIX 9 AA9 ALA A 260 GLN A 273 1 14 HELIX 10 AB1 THR A 292 CYS A 300 1 9 SHEET 1 AA1 6 LEU A 67 GLN A 69 0 SHEET 2 AA1 6 MET A 17 THR A 21 -1 N THR A 21 O LEU A 67 SHEET 3 AA1 6 THR A 26 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 4 AA1 6 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 5 AA1 6 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38 SHEET 6 AA1 6 VAL A 77 GLN A 83 -1 N GLN A 83 O VAL A 86 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ILE A 152 -1 N ASN A 151 O SER A 158 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N LEU A 115 O VAL A 148 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 LINK NE2 HIS A 41 ZN ZN A 503 1555 1555 2.13 LINK SG CYS A 145 ZN ZN A 503 1555 1555 2.51 LINK ZN ZN A 503 O HOH A 642 1555 1555 2.66 CRYST1 114.300 54.290 44.970 90.00 102.12 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 0.008749 0.000000 0.001879 0.00000 SCALE2 0.000000 0.018420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022744 0.00000