HEADER VIRAL PROTEIN 24-OCT-20 7DCD TITLE NONSTRUCTURAL PROTEIN 7 AND 8 COMPLEX OF SARS-COV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 7; COMPND 3 CHAIN: A, C, E, G; COMPND 4 SYNONYM: NSP7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: NON-STRUCTURAL PROTEIN 8; COMPND 8 CHAIN: B, D, F, H; COMPND 9 SYNONYM: NSP8; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 10 2; SOURCE 11 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 12 ORGANISM_TAXID: 2697049; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, NSP7, NSP8, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.H.ZHANG,L.LI,D.SU REVDAT 3 29-NOV-23 7DCD 1 REMARK REVDAT 2 07-APR-21 7DCD 1 JRNL REVDAT 1 24-MAR-21 7DCD 0 JRNL AUTH C.ZHANG,L.LI,J.HE,C.CHEN,D.SU JRNL TITL NONSTRUCTURAL PROTEIN 7 AND 8 COMPLEXES OF SARS-COV-2. JRNL REF PROTEIN SCI. V. 30 873 2021 JRNL REFN ESSN 1469-896X JRNL PMID 33594727 JRNL DOI 10.1002/PRO.4046 REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX PHENIX1.18-3845 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 20420 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.254 REMARK 3 FREE R VALUE : 0.353 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.440 REMARK 3 FREE R VALUE TEST SET COUNT : 906 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 41.0700 - 4.6687 0.91 3193 144 0.2010 0.2663 REMARK 3 2 4.6687 - 3.7065 0.85 2981 131 0.2265 0.3277 REMARK 3 3 3.7065 - 3.2382 0.94 3300 123 0.2680 0.3711 REMARK 3 4 3.2382 - 2.9422 0.98 3411 171 0.3049 0.4485 REMARK 3 5 2.9422 - 2.7314 0.98 3376 203 0.3392 0.4512 REMARK 3 6 2.7314 - 2.5703 0.93 3253 134 0.3299 0.4657 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.82 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 : 0.010 5873 REMARK 3 ANGLE : 1.239 7991 REMARK 3 CHIRALITY : 0.059 1019 REMARK 3 PLANARITY : 0.005 999 REMARK 3 DIHEDRAL : 4.335 3639 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 7DCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1300019128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8.2 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) : 0.97930 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20420 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 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 (%) : 93.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: 2AHM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM SODIUM CHLORIDE, 100MM TRIS-HCL, REMARK 280 PH 8.2, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: 2930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 REMARK 350 BIOMOLECULE: 2 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: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 REMARK 350 BIOMOLECULE: 3 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: 2720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 REMARK 350 BIOMOLECULE: 4 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: 2740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 SER A 1 REMARK 465 LYS A 2 REMARK 465 ASN A 78 REMARK 465 ARG A 79 REMARK 465 ALA A 80 REMARK 465 THR A 81 REMARK 465 LEU A 82 REMARK 465 GLN A 83 REMARK 465 SER B 193 REMARK 465 ALA B 194 REMARK 465 VAL B 195 REMARK 465 LYS B 196 REMARK 465 LEU B 197 REMARK 465 GLN B 198 REMARK 465 SER C 1 REMARK 465 ASN C 78 REMARK 465 ARG C 79 REMARK 465 ALA C 80 REMARK 465 THR C 81 REMARK 465 LEU C 82 REMARK 465 GLN C 83 REMARK 465 SER D 193 REMARK 465 ALA D 194 REMARK 465 VAL D 195 REMARK 465 LYS D 196 REMARK 465 LEU D 197 REMARK 465 GLN D 198 REMARK 465 SER E 1 REMARK 465 LYS E 2 REMARK 465 ARG E 79 REMARK 465 ALA E 80 REMARK 465 THR E 81 REMARK 465 LEU E 82 REMARK 465 GLN E 83 REMARK 465 ARG F 190 REMARK 465 ALA F 191 REMARK 465 ASN F 192 REMARK 465 SER F 193 REMARK 465 ALA F 194 REMARK 465 VAL F 195 REMARK 465 LYS F 196 REMARK 465 LEU F 197 REMARK 465 GLN F 198 REMARK 465 SER G 1 REMARK 465 LYS G 2 REMARK 465 ASN G 78 REMARK 465 ARG G 79 REMARK 465 ALA G 80 REMARK 465 THR G 81 REMARK 465 LEU G 82 REMARK 465 GLN G 83 REMARK 465 ALA H 191 REMARK 465 ASN H 192 REMARK 465 SER H 193 REMARK 465 ALA H 194 REMARK 465 VAL H 195 REMARK 465 LYS H 196 REMARK 465 LEU H 197 REMARK 465 GLN H 198 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 27 CG CD CE NZ REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 ASP A 67 CG OD1 OD2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 ARG B 190 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 47 CG CD OE1 OE2 REMARK 470 GLU D 77 CG CD OE1 OE2 REMARK 470 ARG D 96 CG CD NE CZ NH1 NH2 REMARK 470 LEU D 153 CG CD1 CD2 REMARK 470 ILE D 166 CG1 CG2 CD1 REMARK 470 LYS E 27 CG CD CE NZ REMARK 470 LEU E 41 CG CD1 CD2 REMARK 470 GLU E 73 CG CD OE1 OE2 REMARK 470 LYS G 27 CG CD CE NZ REMARK 470 LYS G 43 CG CD CE NZ REMARK 470 LYS H 79 CG CD CE NZ REMARK 470 LYS H 82 CG CD CE NZ REMARK 470 LYS H 127 CG CD CE NZ REMARK 470 GLN H 157 CG CD OE1 NE2 REMARK 470 LYS H 165 CG CD CE NZ 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 OE1 GLN G 19 OG1 THR H 84 1.95 REMARK 500 OD1 ASP B 112 O HOH B 201 2.03 REMARK 500 O SER E 54 OG SER E 57 2.06 REMARK 500 O VAL G 58 OG SER G 61 2.08 REMARK 500 O SER E 25 N LYS E 27 2.10 REMARK 500 O GLN G 19 NH2 ARG H 80 2.12 REMARK 500 O SER D 85 OG1 THR D 89 2.12 REMARK 500 NE2 GLN A 18 OE2 GLU A 23 2.13 REMARK 500 NE2 GLN E 18 OE2 GLU E 23 2.19 REMARK 500 OD1 ASN H 176 ND2 ASN H 179 2.19 REMARK 500 O SER A 54 OG SER A 57 2.19 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 NZ LYS A 7 CG MET D 90 1655 1.76 REMARK 500 NZ LYS A 7 CE MET D 90 1655 1.96 REMARK 500 NZ LYS A 7 CB MET D 90 1655 2.02 REMARK 500 OG1 THR C 45 O ASP D 163 1455 2.12 REMARK 500 NZ LYS A 7 SD MET D 90 1655 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 CYS C 32 CB CYS C 32 SG -0.098 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 CYS A 8 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 ILE D 172 N - CA - C ANGL. DEV. = -26.1 DEGREES REMARK 500 LEU F 122 N - CA - C ANGL. DEV. = -17.5 DEGREES REMARK 500 THR F 123 N - CA - CB ANGL. DEV. = 23.0 DEGREES REMARK 500 LEU G 20 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 SER G 26 CB - CA - C ANGL. DEV. = 23.8 DEGREES REMARK 500 LYS H 97 CB - CA - C ANGL. DEV. = 20.1 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 SER A 26 -61.79 53.63 REMARK 500 ALA B 150 34.85 70.41 REMARK 500 GLN B 157 29.74 -178.55 REMARK 500 GLN B 158 103.07 -170.97 REMARK 500 SER B 164 58.98 25.65 REMARK 500 ALA B 181 77.30 -109.02 REMARK 500 MET C 3 0.14 -66.86 REMARK 500 ARG C 21 47.53 71.16 REMARK 500 SER C 24 7.50 53.95 REMARK 500 SER C 26 -62.07 71.11 REMARK 500 LYS D 79 -61.46 -92.29 REMARK 500 LYS D 97 0.37 -66.27 REMARK 500 ALA D 125 12.09 49.68 REMARK 500 THR D 141 -32.06 -132.41 REMARK 500 SER D 151 13.17 56.76 REMARK 500 GLN D 158 149.28 -176.94 REMARK 500 SER D 164 15.39 56.56 REMARK 500 LEU D 189 -159.70 -117.35 REMARK 500 SER E 24 36.90 -75.32 REMARK 500 SER E 26 32.87 -54.42 REMARK 500 LYS E 27 -61.58 -142.58 REMARK 500 ASP F 99 53.53 32.74 REMARK 500 ASN F 118 -169.72 -124.46 REMARK 500 ASP F 143 88.94 -161.14 REMARK 500 SER F 151 41.08 35.43 REMARK 500 GLN F 157 -9.84 -143.20 REMARK 500 GLN F 158 89.73 -165.64 REMARK 500 ASP F 161 -160.97 -109.45 REMARK 500 ASP F 163 36.92 -98.14 REMARK 500 SER F 164 8.55 59.23 REMARK 500 ALA F 181 72.62 -103.82 REMARK 500 ARG G 21 75.14 73.86 REMARK 500 SER G 25 65.18 -168.85 REMARK 500 HIS G 36 -39.47 -38.67 REMARK 500 LYS G 43 -30.13 -134.87 REMARK 500 ASP H 99 18.03 49.51 REMARK 500 ASP H 112 42.02 -93.56 REMARK 500 ASN H 118 163.37 177.53 REMARK 500 CYS H 142 142.93 -170.92 REMARK 500 SER H 151 19.27 52.26 REMARK 500 GLN H 158 108.34 -164.48 REMARK 500 ALA H 162 56.82 -93.84 REMARK 500 ASP H 163 5.35 -175.10 REMARK 500 SER H 177 -76.08 -24.33 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 108 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH C 103 DISTANCE = 7.05 ANGSTROMS REMARK 525 HOH C 104 DISTANCE = 9.29 ANGSTROMS REMARK 525 HOH F 210 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH F 211 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH G 112 DISTANCE = 8.78 ANGSTROMS REMARK 525 HOH H 212 DISTANCE = 7.40 ANGSTROMS DBREF 7DCD A 1 83 UNP P0DTC1 R1A_SARS2 3860 3942 DBREF 7DCD B 77 198 UNP P0DTC1 R1A_SARS2 4019 4140 DBREF 7DCD C 1 83 UNP P0DTC1 R1A_SARS2 3860 3942 DBREF 7DCD D 77 198 UNP P0DTC1 R1A_SARS2 4019 4140 DBREF 7DCD E 1 83 UNP P0DTC1 R1A_SARS2 3860 3942 DBREF 7DCD F 77 198 UNP P0DTC1 R1A_SARS2 4019 4140 DBREF 7DCD G 1 83 UNP P0DTC1 R1A_SARS2 3860 3942 DBREF 7DCD H 77 198 UNP P0DTC1 R1A_SARS2 4019 4140 SEQRES 1 A 83 SER LYS MET SER ASP VAL LYS CYS THR SER VAL VAL LEU SEQRES 2 A 83 LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SER SER SER SEQRES 3 A 83 LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS ASN ASP ILE SEQRES 4 A 83 LEU LEU ALA LYS ASP THR THR GLU ALA PHE GLU LYS MET SEQRES 5 A 83 VAL SER LEU LEU SER VAL LEU LEU SER MET GLN GLY ALA SEQRES 6 A 83 VAL ASP ILE ASN LYS LEU CYS GLU GLU MET LEU ASP ASN SEQRES 7 A 83 ARG ALA THR LEU GLN SEQRES 1 B 122 GLU ASP LYS ARG ALA LYS VAL THR SER ALA MET GLN THR SEQRES 2 B 122 MET LEU PHE THR MET LEU ARG LYS LEU ASP ASN ASP ALA SEQRES 3 B 122 LEU ASN ASN ILE ILE ASN ASN ALA ARG ASP GLY CYS VAL SEQRES 4 B 122 PRO LEU ASN ILE ILE PRO LEU THR THR ALA ALA LYS LEU SEQRES 5 B 122 MET VAL VAL ILE PRO ASP TYR ASN THR TYR LYS ASN THR SEQRES 6 B 122 CYS ASP GLY THR THR PHE THR TYR ALA SER ALA LEU TRP SEQRES 7 B 122 GLU ILE GLN GLN VAL VAL ASP ALA ASP SER LYS ILE VAL SEQRES 8 B 122 GLN LEU SER GLU ILE SER MET ASP ASN SER PRO ASN LEU SEQRES 9 B 122 ALA TRP PRO LEU ILE VAL THR ALA LEU ARG ALA ASN SER SEQRES 10 B 122 ALA VAL LYS LEU GLN SEQRES 1 C 83 SER LYS MET SER ASP VAL LYS CYS THR SER VAL VAL LEU SEQRES 2 C 83 LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SER SER SER SEQRES 3 C 83 LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS ASN ASP ILE SEQRES 4 C 83 LEU LEU ALA LYS ASP THR THR GLU ALA PHE GLU LYS MET SEQRES 5 C 83 VAL SER LEU LEU SER VAL LEU LEU SER MET GLN GLY ALA SEQRES 6 C 83 VAL ASP ILE ASN LYS LEU CYS GLU GLU MET LEU ASP ASN SEQRES 7 C 83 ARG ALA THR LEU GLN SEQRES 1 D 122 GLU ASP LYS ARG ALA LYS VAL THR SER ALA MET GLN THR SEQRES 2 D 122 MET LEU PHE THR MET LEU ARG LYS LEU ASP ASN ASP ALA SEQRES 3 D 122 LEU ASN ASN ILE ILE ASN ASN ALA ARG ASP GLY CYS VAL SEQRES 4 D 122 PRO LEU ASN ILE ILE PRO LEU THR THR ALA ALA LYS LEU SEQRES 5 D 122 MET VAL VAL ILE PRO ASP TYR ASN THR TYR LYS ASN THR SEQRES 6 D 122 CYS ASP GLY THR THR PHE THR TYR ALA SER ALA LEU TRP SEQRES 7 D 122 GLU ILE GLN GLN VAL VAL ASP ALA ASP SER LYS ILE VAL SEQRES 8 D 122 GLN LEU SER GLU ILE SER MET ASP ASN SER PRO ASN LEU SEQRES 9 D 122 ALA TRP PRO LEU ILE VAL THR ALA LEU ARG ALA ASN SER SEQRES 10 D 122 ALA VAL LYS LEU GLN SEQRES 1 E 83 SER LYS MET SER ASP VAL LYS CYS THR SER VAL VAL LEU SEQRES 2 E 83 LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SER SER SER SEQRES 3 E 83 LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS ASN ASP ILE SEQRES 4 E 83 LEU LEU ALA LYS ASP THR THR GLU ALA PHE GLU LYS MET SEQRES 5 E 83 VAL SER LEU LEU SER VAL LEU LEU SER MET GLN GLY ALA SEQRES 6 E 83 VAL ASP ILE ASN LYS LEU CYS GLU GLU MET LEU ASP ASN SEQRES 7 E 83 ARG ALA THR LEU GLN SEQRES 1 F 122 GLU ASP LYS ARG ALA LYS VAL THR SER ALA MET GLN THR SEQRES 2 F 122 MET LEU PHE THR MET LEU ARG LYS LEU ASP ASN ASP ALA SEQRES 3 F 122 LEU ASN ASN ILE ILE ASN ASN ALA ARG ASP GLY CYS VAL SEQRES 4 F 122 PRO LEU ASN ILE ILE PRO LEU THR THR ALA ALA LYS LEU SEQRES 5 F 122 MET VAL VAL ILE PRO ASP TYR ASN THR TYR LYS ASN THR SEQRES 6 F 122 CYS ASP GLY THR THR PHE THR TYR ALA SER ALA LEU TRP SEQRES 7 F 122 GLU ILE GLN GLN VAL VAL ASP ALA ASP SER LYS ILE VAL SEQRES 8 F 122 GLN LEU SER GLU ILE SER MET ASP ASN SER PRO ASN LEU SEQRES 9 F 122 ALA TRP PRO LEU ILE VAL THR ALA LEU ARG ALA ASN SER SEQRES 10 F 122 ALA VAL LYS LEU GLN SEQRES 1 G 83 SER LYS MET SER ASP VAL LYS CYS THR SER VAL VAL LEU SEQRES 2 G 83 LEU SER VAL LEU GLN GLN LEU ARG VAL GLU SER SER SER SEQRES 3 G 83 LYS LEU TRP ALA GLN CYS VAL GLN LEU HIS ASN ASP ILE SEQRES 4 G 83 LEU LEU ALA LYS ASP THR THR GLU ALA PHE GLU LYS MET SEQRES 5 G 83 VAL SER LEU LEU SER VAL LEU LEU SER MET GLN GLY ALA SEQRES 6 G 83 VAL ASP ILE ASN LYS LEU CYS GLU GLU MET LEU ASP ASN SEQRES 7 G 83 ARG ALA THR LEU GLN SEQRES 1 H 122 GLU ASP LYS ARG ALA LYS VAL THR SER ALA MET GLN THR SEQRES 2 H 122 MET LEU PHE THR MET LEU ARG LYS LEU ASP ASN ASP ALA SEQRES 3 H 122 LEU ASN ASN ILE ILE ASN ASN ALA ARG ASP GLY CYS VAL SEQRES 4 H 122 PRO LEU ASN ILE ILE PRO LEU THR THR ALA ALA LYS LEU SEQRES 5 H 122 MET VAL VAL ILE PRO ASP TYR ASN THR TYR LYS ASN THR SEQRES 6 H 122 CYS ASP GLY THR THR PHE THR TYR ALA SER ALA LEU TRP SEQRES 7 H 122 GLU ILE GLN GLN VAL VAL ASP ALA ASP SER LYS ILE VAL SEQRES 8 H 122 GLN LEU SER GLU ILE SER MET ASP ASN SER PRO ASN LEU SEQRES 9 H 122 ALA TRP PRO LEU ILE VAL THR ALA LEU ARG ALA ASN SER SEQRES 10 H 122 ALA VAL LYS LEU GLN FORMUL 9 HOH *75(H2 O) HELIX 1 AA1 MET A 3 LEU A 20 1 18 HELIX 2 AA2 SER A 26 LEU A 41 1 16 HELIX 3 AA3 ASP A 44 SER A 61 1 18 HELIX 4 AA4 ASP A 67 LEU A 76 1 10 HELIX 5 AA5 ASP B 78 ASP B 99 1 22 HELIX 6 AA6 ASN B 100 ALA B 110 1 11 HELIX 7 AA7 ARG B 111 GLY B 113 5 3 HELIX 8 AA8 ASP B 134 THR B 141 1 8 HELIX 9 AA9 GLN B 168 ILE B 172 5 5 HELIX 10 AB1 ASN B 176 LEU B 180 5 5 HELIX 11 AB2 MET C 3 LEU C 20 1 18 HELIX 12 AB3 LEU C 28 LEU C 41 1 14 HELIX 13 AB4 ASP C 44 SER C 61 1 18 HELIX 14 AB5 ASP C 67 ASP C 77 1 11 HELIX 15 AB6 LYS D 79 LYS D 97 1 19 HELIX 16 AB7 ASN D 100 ASP D 112 1 13 HELIX 17 AB8 ASP D 134 ASN D 140 1 7 HELIX 18 AB9 GLN D 168 ILE D 172 5 5 HELIX 19 AC1 ASN D 176 LEU D 180 5 5 HELIX 20 AC2 ASP E 5 GLN E 19 1 15 HELIX 21 AC3 LYS E 27 ALA E 42 1 16 HELIX 22 AC4 THR E 46 MET E 62 1 17 HELIX 23 AC5 ASP E 67 ASP E 77 1 11 HELIX 24 AC6 ASP F 78 LYS F 97 1 20 HELIX 25 AC7 ASN F 100 ASP F 112 1 13 HELIX 26 AC8 ASP F 134 THR F 141 1 8 HELIX 27 AC9 GLN F 168 ILE F 172 5 5 HELIX 28 AD1 ASN F 176 LEU F 180 5 5 HELIX 29 AD2 SER G 4 ARG G 21 1 18 HELIX 30 AD3 SER G 25 ALA G 42 1 18 HELIX 31 AD4 ASP G 44 LEU G 60 1 17 HELIX 32 AD5 ASP G 67 ASP G 77 1 11 HELIX 33 AD6 LYS H 79 LEU H 98 1 20 HELIX 34 AD7 ASN H 100 ASP H 112 1 13 HELIX 35 AD8 ASP H 134 CYS H 142 1 9 HELIX 36 AD9 GLN H 168 ILE H 172 5 5 HELIX 37 AE1 ASN H 176 LEU H 180 5 5 SHEET 1 AA1 5 LYS B 127 ILE B 132 0 SHEET 2 AA1 5 LEU B 184 ARG B 190 -1 O LEU B 184 N ILE B 132 SHEET 3 AA1 5 TRP B 154 VAL B 160 -1 N GLU B 155 O LEU B 189 SHEET 4 AA1 5 THR B 146 PHE B 147 -1 N PHE B 147 O TRP B 154 SHEET 5 AA1 5 CYS B 142 ASP B 143 -1 N ASP B 143 O THR B 146 SHEET 1 AA2 5 LEU D 128 ILE D 132 0 SHEET 2 AA2 5 LEU D 184 LEU D 189 -1 O LEU D 184 N ILE D 132 SHEET 3 AA2 5 ALA D 152 VAL D 160 -1 N VAL D 160 O ILE D 185 SHEET 4 AA2 5 THR D 146 TYR D 149 -1 N PHE D 147 O TRP D 154 SHEET 5 AA2 5 CYS D 142 ASP D 143 -1 N ASP D 143 O THR D 146 SHEET 1 AA3 4 LEU D 128 ILE D 132 0 SHEET 2 AA3 4 LEU D 184 LEU D 189 -1 O LEU D 184 N ILE D 132 SHEET 3 AA3 4 ALA D 152 VAL D 160 -1 N VAL D 160 O ILE D 185 SHEET 4 AA3 4 ILE D 166 VAL D 167 -1 O VAL D 167 N VAL D 159 SHEET 1 AA4 5 LEU F 128 ILE F 132 0 SHEET 2 AA4 5 LEU F 184 LEU F 189 -1 O VAL F 186 N VAL F 130 SHEET 3 AA4 5 ALA F 152 VAL F 160 -1 N GLN F 157 O THR F 187 SHEET 4 AA4 5 THR F 146 TYR F 149 -1 N PHE F 147 O TRP F 154 SHEET 5 AA4 5 CYS F 142 ASP F 143 -1 N ASP F 143 O THR F 146 SHEET 1 AA5 4 LEU F 128 ILE F 132 0 SHEET 2 AA5 4 LEU F 184 LEU F 189 -1 O VAL F 186 N VAL F 130 SHEET 3 AA5 4 ALA F 152 VAL F 160 -1 N GLN F 157 O THR F 187 SHEET 4 AA5 4 ILE F 166 VAL F 167 -1 O VAL F 167 N VAL F 159 SHEET 1 AA6 4 LEU H 128 ILE H 132 0 SHEET 2 AA6 4 LEU H 184 LEU H 189 -1 O LEU H 184 N ILE H 132 SHEET 3 AA6 4 ALA H 152 VAL H 160 -1 N GLU H 155 O LEU H 189 SHEET 4 AA6 4 THR H 146 TYR H 149 -1 N TYR H 149 O ALA H 152 SHEET 1 AA7 4 LEU H 128 ILE H 132 0 SHEET 2 AA7 4 LEU H 184 LEU H 189 -1 O LEU H 184 N ILE H 132 SHEET 3 AA7 4 ALA H 152 VAL H 160 -1 N GLU H 155 O LEU H 189 SHEET 4 AA7 4 ILE H 166 VAL H 167 -1 O VAL H 167 N VAL H 159 SSBOND 1 CYS A 8 CYS C 8 1555 1655 2.04 SSBOND 2 CYS E 8 CYS G 8 1555 1545 2.02 CISPEP 1 TRP B 182 PRO B 183 0 5.41 CISPEP 2 TRP D 182 PRO D 183 0 4.21 CISPEP 3 TRP F 182 PRO F 183 0 0.55 CISPEP 4 TRP H 182 PRO H 183 0 3.37 CRYST1 43.031 42.990 100.630 90.01 90.03 72.61 P 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 0.023239 -0.007277 0.000014 0.00000 SCALE2 0.000000 0.024375 0.000001 0.00000 SCALE3 0.000000 0.000000 0.009937 0.00000