HEADER HYDROLASE 15-APR-21 7MHN TITLE ENSEMBLE REFINEMENT STRUCTURE OF SARS-COV-2 MAIN PROTEASE (MPRO) AT TITLE 2 277 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 45 AUTHOR A.EBRAHIM,B.T.RILEY,D.KUMARAN,B.ANDI,M.R.FUCHS,S.MCSWEENEY,D.A.KEEDY REVDAT 5 18-OCT-23 7MHN 1 REMARK REVDAT 4 07-SEP-22 7MHN 1 JRNL REVDAT 3 06-APR-22 7MHN 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 7MHN 1 JRNL REVDAT 1 12-MAY-21 7MHN 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. 2.19 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 14037 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.215 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 48.9600 - 3.7500 1.00 2736 138 0.1227 0.1474 REMARK 3 2 3.7500 - 2.9700 1.00 2691 153 0.1458 0.2269 REMARK 3 3 2.9700 - 2.6000 0.99 2637 157 0.1799 0.2539 REMARK 3 4 2.6000 - 2.3600 0.99 2612 143 0.1955 0.3242 REMARK 3 5 2.3600 - 2.1908 0.99 2623 147 0.2234 0.2927 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 7MHN 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_1000255381. 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) : 277 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 0.5.902-GFFA11588-DIALS REMARK 200 -1.14 REMARK 200 DATA SCALING SOFTWARE : DIALS 1.14.13-G10ECFBB15-RELEASE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14120 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.191 REMARK 200 RESOLUTION RANGE LOW (A) : 48.962 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.928 REMARK 200 R MERGE (I) : 0.29160 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.4679 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.87 REMARK 200 R MERGE FOR SHELL (I) : 1.80540 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.105 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 (%): 39.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 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 57.51150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.51150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.17900 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: 4180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25440 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 523 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 2 CYS A 16 CB CYS A 16 SG -0.118 REMARK 500 3 CYS A 145 CB CYS A 145 SG 0.129 REMARK 500 4 CYS A 16 CB CYS A 16 SG -0.100 REMARK 500 5 CYS A 16 CB CYS A 16 SG -0.101 REMARK 500 5 GLU A 166 CG GLU A 166 CD 0.107 REMARK 500 6 CYS A 156 CB CYS A 156 SG 0.121 REMARK 500 7 CYS A 16 CB CYS A 16 SG -0.112 REMARK 500 7 GLU A 47 CB GLU A 47 CG 0.142 REMARK 500 7 GLU A 47 CG GLU A 47 CD 0.096 REMARK 500 7 CYS A 156 CB CYS A 156 SG 0.135 REMARK 500 8 CYS A 145 CB CYS A 145 SG 0.216 REMARK 500 8 CYS A 156 CB CYS A 156 SG -0.177 REMARK 500 11 CYS A 300 CB CYS A 300 SG -0.135 REMARK 500 12 CYS A 16 CB CYS A 16 SG -0.104 REMARK 500 14 CYS A 265 CB CYS A 265 SG -0.097 REMARK 500 15 CYS A 16 CB CYS A 16 SG -0.136 REMARK 500 15 GLU A 166 CB GLU A 166 CG 0.123 REMARK 500 17 MET A 165 CB MET A 165 CG 0.233 REMARK 500 17 CYS A 300 CB CYS A 300 SG 0.122 REMARK 500 18 CYS A 145 CB CYS A 145 SG -0.141 REMARK 500 19 CYS A 300 CB CYS A 300 SG 0.106 REMARK 500 20 CYS A 145 CB CYS A 145 SG 0.115 REMARK 500 20 CYS A 300 CB CYS A 300 SG 0.108 REMARK 500 21 CYS A 145 CB CYS A 145 SG 0.120 REMARK 500 22 CYS A 145 CB CYS A 145 SG -0.111 REMARK 500 23 TYR A 118 CE2 TYR A 118 CD2 -0.092 REMARK 500 23 CYS A 156 CB CYS A 156 SG -0.117 REMARK 500 25 GLU A 288 CB GLU A 288 CG 0.137 REMARK 500 25 GLU A 288 CG GLU A 288 CD 0.111 REMARK 500 25 CYS A 300 CB CYS A 300 SG 0.139 REMARK 500 27 GLU A 290 CB GLU A 290 CG 0.134 REMARK 500 28 CYS A 145 CB CYS A 145 SG -0.099 REMARK 500 29 CYS A 44 CB CYS A 44 SG -0.134 REMARK 500 29 CYS A 117 CB CYS A 117 SG -0.100 REMARK 500 29 CYS A 145 CB CYS A 145 SG 0.231 REMARK 500 32 CYS A 300 CB CYS A 300 SG 0.117 REMARK 500 33 CYS A 44 CB CYS A 44 SG -0.098 REMARK 500 33 CYS A 156 CB CYS A 156 SG -0.097 REMARK 500 34 CYS A 16 CB CYS A 16 SG -0.105 REMARK 500 34 CYS A 300 CB CYS A 300 SG 0.105 REMARK 500 35 CYS A 16 CB CYS A 16 SG -0.103 REMARK 500 35 VAL A 104 CB VAL A 104 CG1 -0.175 REMARK 500 36 CYS A 117 CB CYS A 117 SG -0.099 REMARK 500 37 CYS A 156 CB CYS A 156 SG 0.214 REMARK 500 38 CYS A 117 CB CYS A 117 SG -0.106 REMARK 500 38 CYS A 300 CB CYS A 300 SG 0.135 REMARK 500 39 CYS A 300 CB CYS A 300 SG 0.127 REMARK 500 44 CYS A 128 CB CYS A 128 SG -0.221 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 16 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 3 CYS A 145 CA - CB - SG ANGL. DEV. = 10.2 DEGREES REMARK 500 3 ASP A 155 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 4 ASP A 153 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 4 ASP A 155 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 4 ASP A 155 CB - CG - OD2 ANGL. DEV. = -8.9 DEGREES REMARK 500 5 LEU A 75 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 5 ASP A 153 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 6 CYS A 16 CA - CB - SG ANGL. DEV. = 8.9 DEGREES REMARK 500 6 CYS A 300 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 8 CYS A 145 CA - CB - SG ANGL. DEV. = 11.2 DEGREES REMARK 500 9 CYS A 145 CA - CB - SG ANGL. DEV. = 11.8 DEGREES REMARK 500 12 MET A 6 CA - CB - CG ANGL. DEV. = 11.5 DEGREES REMARK 500 12 LEU A 286 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 14 CYS A 300 CA - CB - SG ANGL. DEV. = -13.4 DEGREES REMARK 500 15 CYS A 300 CA - CB - SG ANGL. DEV. = 9.5 DEGREES REMARK 500 16 CYS A 145 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 17 ASP A 153 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 18 LEU A 67 CA - CB - CG ANGL. DEV. = 18.0 DEGREES REMARK 500 19 CYS A 145 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 20 MET A 17 CG - SD - CE ANGL. DEV. = 11.0 DEGREES REMARK 500 20 CYS A 145 CA - CB - SG ANGL. DEV. = 9.2 DEGREES REMARK 500 20 CYS A 300 CA - CB - SG ANGL. DEV. = 8.7 DEGREES REMARK 500 22 LEU A 262 CA - CB - CG ANGL. DEV. = -14.1 DEGREES REMARK 500 22 CYS A 300 CA - CB - SG ANGL. DEV. = 10.1 DEGREES REMARK 500 23 MET A 17 CG - SD - CE ANGL. DEV. = 10.1 DEGREES REMARK 500 25 CYS A 44 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 25 CYS A 300 CA - CB - SG ANGL. DEV. = 9.3 DEGREES REMARK 500 25 PHE A 305 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 26 PHE A 305 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 26 PHE A 305 CB - CG - CD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 28 CYS A 16 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 28 ASP A 229 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 30 CYS A 300 CA - CB - SG ANGL. DEV. = 13.0 DEGREES REMARK 500 34 CYS A 145 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 35 CYS A 22 CA - CB - SG ANGL. DEV. = 10.4 DEGREES REMARK 500 35 CYS A 300 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 38 CYS A 145 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 38 TYR A 154 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 38 CYS A 156 CA - CB - SG ANGL. DEV. = 9.4 DEGREES REMARK 500 38 MET A 165 CA - CB - CG ANGL. DEV. = 11.5 DEGREES REMARK 500 39 ASP A 197 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 39 CYS A 300 CA - CB - SG ANGL. DEV. = 8.5 DEGREES REMARK 500 39 PHE A 305 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 40 CYS A 300 CA - CB - SG ANGL. DEV. = 12.8 DEGREES REMARK 500 42 PRO A 122 C - N - CD ANGL. DEV. = -13.8 DEGREES REMARK 500 43 CYS A 128 CA - CB - SG ANGL. DEV. = 8.5 DEGREES REMARK 500 45 LEU A 67 CA - CB - CG ANGL. DEV. = 16.5 DEGREES REMARK 500 45 CYS A 300 CA - CB - SG ANGL. DEV. = -12.5 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 1 THR A 24 -73.54 108.71 REMARK 500 1 ASP A 33 -130.87 32.16 REMARK 500 1 ILE A 59 1.45 -68.71 REMARK 500 1 LYS A 61 -143.77 -76.95 REMARK 500 1 SER A 62 156.38 159.42 REMARK 500 1 ASN A 63 46.65 -53.76 REMARK 500 1 HIS A 64 -31.53 -164.89 REMARK 500 1 ASN A 65 15.96 -62.81 REMARK 500 1 ASN A 72 -109.14 -38.68 REMARK 500 1 VAL A 73 104.34 27.22 REMARK 500 1 ILE A 78 -19.50 -159.19 REMARK 500 1 SER A 81 161.00 159.31 REMARK 500 1 ASN A 84 -115.67 56.40 REMARK 500 1 ASN A 151 -91.41 -83.93 REMARK 500 1 ILE A 152 -66.47 -163.17 REMARK 500 1 ASP A 153 -69.59 113.16 REMARK 500 1 TYR A 154 108.62 148.90 REMARK 500 1 ASP A 155 -2.02 44.79 REMARK 500 1 PRO A 168 0.05 -68.10 REMARK 500 1 ARG A 188 123.99 -173.06 REMARK 500 1 GLN A 189 95.10 -68.82 REMARK 500 1 ALA A 191 95.09 -68.27 REMARK 500 1 LEU A 227 -73.65 -43.31 REMARK 500 1 ASN A 228 -59.93 -28.24 REMARK 500 1 THR A 243 -163.64 -102.02 REMARK 500 1 LYS A 269 -50.26 -27.99 REMARK 500 1 ASN A 274 -146.10 -107.88 REMARK 500 1 MET A 276 76.38 -36.29 REMARK 500 1 ARG A 279 -158.36 -106.80 REMARK 500 1 GLN A 299 16.55 -59.97 REMARK 500 1 SER A 301 -79.23 177.41 REMARK 500 1 VAL A 303 50.50 -150.80 REMARK 500 1 PHE A 305 113.60 -24.93 REMARK 500 2 THR A 24 -35.81 89.72 REMARK 500 2 ASP A 33 -115.32 55.20 REMARK 500 2 SER A 46 -5.67 -55.61 REMARK 500 2 ASN A 51 65.78 -171.74 REMARK 500 2 ASN A 63 76.16 -61.63 REMARK 500 2 HIS A 64 -13.64 154.32 REMARK 500 2 ASN A 72 -149.50 -64.48 REMARK 500 2 VAL A 73 120.99 44.41 REMARK 500 2 ASN A 84 -123.91 58.15 REMARK 500 2 THR A 98 116.14 -23.91 REMARK 500 2 ASN A 119 15.10 56.75 REMARK 500 2 PHE A 150 117.44 -161.99 REMARK 500 2 ILE A 152 -31.14 135.44 REMARK 500 2 ASP A 153 -92.47 64.65 REMARK 500 2 TYR A 154 87.01 -166.27 REMARK 500 2 ASP A 155 -17.34 47.22 REMARK 500 2 CYS A 156 169.90 -42.36 REMARK 500 REMARK 500 THIS ENTRY HAS 1418 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 ASN A 72 VAL A 73 1 138.74 REMARK 500 VAL A 73 GLN A 74 1 137.18 REMARK 500 ASN A 151 ILE A 152 1 138.64 REMARK 500 GLY A 195 THR A 196 1 -143.45 REMARK 500 GLY A 275 MET A 276 1 -146.85 REMARK 500 VAL A 303 THR A 304 1 122.33 REMARK 500 HIS A 64 ASN A 65 2 149.09 REMARK 500 ASP A 155 CYS A 156 2 124.06 REMARK 500 SER A 158 PHE A 159 2 149.20 REMARK 500 PRO A 184 PHE A 185 2 142.35 REMARK 500 ASP A 216 ARG A 217 2 -145.44 REMARK 500 ASN A 221 ARG A 222 2 145.24 REMARK 500 SER A 301 GLY A 302 2 -142.30 REMARK 500 GLY A 302 VAL A 303 2 144.61 REMARK 500 VAL A 303 THR A 304 2 127.81 REMARK 500 CYS A 22 GLY A 23 3 -149.86 REMARK 500 ASP A 155 CYS A 156 3 133.24 REMARK 500 ASP A 187 ARG A 188 3 -149.37 REMARK 500 LEU A 220 ASN A 221 3 -148.49 REMARK 500 ARG A 222 PHE A 223 3 141.02 REMARK 500 THR A 24 THR A 25 4 140.26 REMARK 500 LEU A 75 ARG A 76 4 -138.19 REMARK 500 ASN A 142 GLY A 143 4 -137.05 REMARK 500 SER A 158 PHE A 159 4 -141.86 REMARK 500 GLY A 195 THR A 196 4 -142.12 REMARK 500 MET A 276 ASN A 277 4 128.27 REMARK 500 SER A 301 GLY A 302 4 -148.40 REMARK 500 GLY A 302 VAL A 303 4 -146.94 REMARK 500 PHE A 305 GLN A 306 4 -122.04 REMARK 500 THR A 25 THR A 26 5 -145.72 REMARK 500 ILE A 152 ASP A 153 5 146.43 REMARK 500 ASP A 216 ARG A 217 5 -148.60 REMARK 500 ASN A 277 GLY A 278 5 131.24 REMARK 500 VAL A 303 THR A 304 5 144.66 REMARK 500 THR A 24 THR A 25 6 136.85 REMARK 500 ASN A 151 ILE A 152 6 -143.46 REMARK 500 ILE A 152 ASP A 153 6 133.39 REMARK 500 GLY A 195 THR A 196 6 -147.52 REMARK 500 ARG A 222 PHE A 223 6 120.52 REMARK 500 ARG A 279 THR A 280 6 -130.34 REMARK 500 GLY A 302 VAL A 303 6 -146.75 REMARK 500 VAL A 303 THR A 304 6 139.94 REMARK 500 THR A 24 THR A 25 7 147.22 REMARK 500 PHE A 150 ASN A 151 7 146.38 REMARK 500 ASP A 153 TYR A 154 7 143.61 REMARK 500 MET A 165 GLU A 166 7 147.74 REMARK 500 ARG A 279 THR A 280 7 -147.60 REMARK 500 GLY A 302 VAL A 303 7 139.02 REMARK 500 THR A 304 PHE A 305 7 140.83 REMARK 500 THR A 45 SER A 46 8 -147.93 REMARK 500 REMARK 500 THIS ENTRY HAS 365 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 217 0.08 SIDE CHAIN REMARK 500 3 ARG A 298 0.09 SIDE CHAIN REMARK 500 4 ARG A 217 0.09 SIDE CHAIN REMARK 500 6 ARG A 298 0.08 SIDE CHAIN REMARK 500 7 ARG A 60 0.09 SIDE CHAIN REMARK 500 10 ARG A 60 0.09 SIDE CHAIN REMARK 500 10 ARG A 188 0.12 SIDE CHAIN REMARK 500 10 ARG A 298 0.13 SIDE CHAIN REMARK 500 12 ARG A 76 0.08 SIDE CHAIN REMARK 500 17 ARG A 60 0.08 SIDE CHAIN REMARK 500 17 ARG A 298 0.16 SIDE CHAIN REMARK 500 19 ARG A 217 0.10 SIDE CHAIN REMARK 500 24 ARG A 298 0.10 SIDE CHAIN REMARK 500 26 ARG A 217 0.10 SIDE CHAIN REMARK 500 26 ARG A 298 0.11 SIDE CHAIN REMARK 500 33 ARG A 76 0.09 SIDE CHAIN REMARK 500 34 ARG A 60 0.08 SIDE CHAIN REMARK 500 35 ARG A 76 0.10 SIDE CHAIN REMARK 500 36 ARG A 298 0.10 SIDE CHAIN REMARK 500 39 ARG A 217 0.08 SIDE CHAIN REMARK 500 40 ARG A 188 0.11 SIDE CHAIN REMARK 500 40 ARG A 279 0.09 SIDE CHAIN REMARK 500 42 ARG A 188 0.08 SIDE CHAIN REMARK 500 43 ARG A 76 0.08 SIDE CHAIN REMARK 500 44 ARG A 279 0.10 SIDE CHAIN REMARK 500 45 ARG A 217 0.08 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 516 DISTANCE = 6.23 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 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 41 NE2 REMARK 620 2 CYS A 145 SG 107.2 REMARK 620 N 1 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: 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: 7MHQ RELATED DB: PDB REMARK 900 ENSEMBLE REFINEMENT AT 310 K 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 7MHN 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 401 10 HET DMS A 402 10 HET ZN A 403 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 SER A 46 LEU A 50 5 5 HELIX 4 AA4 ASN A 53 ILE A 59 1 7 HELIX 5 AA5 ILE A 200 GLY A 215 1 16 HELIX 6 AA6 THR A 226 TYR A 237 1 12 HELIX 7 AA7 THR A 243 GLY A 258 1 16 HELIX 8 AA8 ALA A 260 ASN A 274 1 15 HELIX 9 AA9 THR A 292 GLN A 299 1 8 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 GLY A 29 N VAL A 18 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 GLY A 79 -1 N GLY A 79 O LYS A 90 SHEET 1 AA2 6 LEU A 67 GLN A 69 0 SHEET 2 AA2 6 MET A 17 THR A 21 -1 N THR A 21 O LEU A 67 SHEET 3 AA2 6 THR A 26 LEU A 32 -1 O GLY A 29 N VAL A 18 SHEET 4 AA2 6 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 5 AA2 6 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38 SHEET 6 AA2 6 MET A 82 GLN A 83 -1 N GLN A 83 O VAL A 86 SHEET 1 AA3 5 TYR A 101 PHE A 103 0 SHEET 2 AA3 5 VAL A 157 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 5 VAL A 148 PHE A 150 -1 N GLY A 149 O CYS A 160 SHEET 4 AA3 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA3 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA4 3 TYR A 101 PHE A 103 0 SHEET 2 AA4 3 VAL A 157 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA4 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 LINK NE2 HIS A 41 ZN ZN A 403 1555 1555 2.43 LINK SG CYS A 145 ZN ZN A 403 1555 1555 2.36 CRYST1 115.023 54.358 44.970 90.00 101.50 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 0.008694 0.000000 0.001769 0.00000 SCALE2 0.000000 0.018397 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022693 0.00000 MODEL 1