HEADER HYDROLASE 27-FEB-21 7LW4 TITLE STRUCTURE OF SARS-COV-2 NSP16/NSP10 COMPLEX IN PRESENCE OF S-ADENOSYL- TITLE 2 L-HOMOCYSTEINE (SAH) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2'-O-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 16,NSP16; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NON-STRUCTURAL PROTEIN 10; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: NSP10,GROWTH FACTOR-LIKE PEPTIDE,GFL; COMPND 11 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 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 11 2; SOURCE 12 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 13 ORGANISM_TAXID: 2697049; SOURCE 14 GENE: REP, 1A-1B; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRODUCT COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.K.GUPTA,T.VISWANATHAN,A.MISRA,S.QI REVDAT 3 18-OCT-23 7LW4 1 REMARK REVDAT 2 17-NOV-21 7LW4 1 JRNL REVDAT 1 05-MAY-21 7LW4 0 JRNL AUTH T.VISWANATHAN,A.MISRA,S.H.CHAN,S.QI,N.DAI,S.ARYA, JRNL AUTH 2 L.MARTINEZ-SOBRIDO,Y.K.GUPTA JRNL TITL A METAL ION ORIENTS SARS-COV-2 MRNA TO ENSURE ACCURATE 2'-O JRNL TITL 2 METHYLATION OF ITS FIRST NUCLEOTIDE. JRNL REF NAT COMMUN V. 12 3287 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34078893 JRNL DOI 10.1038/S41467-021-23594-Y REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38620 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1966 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 29.7500 - 6.0100 1.00 2704 158 0.1968 0.1990 REMARK 3 2 6.0100 - 4.7800 0.99 2660 116 0.1534 0.1608 REMARK 3 3 4.7800 - 4.1800 1.00 2642 140 0.1570 0.2135 REMARK 3 4 4.1700 - 3.7900 1.00 2606 151 0.1887 0.2467 REMARK 3 5 3.7900 - 3.5200 1.00 2663 105 0.2124 0.2506 REMARK 3 6 3.5200 - 3.3200 1.00 2654 131 0.2329 0.2683 REMARK 3 7 3.3100 - 3.1500 1.00 2563 133 0.2371 0.2880 REMARK 3 8 3.1500 - 3.0100 1.00 2568 176 0.2479 0.2865 REMARK 3 9 3.0100 - 2.9000 1.00 2642 132 0.2341 0.2562 REMARK 3 10 2.9000 - 2.8000 1.00 2579 151 0.2578 0.3268 REMARK 3 11 2.8000 - 2.7100 1.00 2584 130 0.2457 0.2712 REMARK 3 12 2.7100 - 2.6300 1.00 2641 132 0.2556 0.3067 REMARK 3 13 2.6300 - 2.5600 1.00 2581 165 0.2572 0.2855 REMARK 3 14 2.5600 - 2.5000 1.00 2567 146 0.2597 0.3168 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.284 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.665 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.58 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 : 0.034 3276 REMARK 3 ANGLE : 2.373 4439 REMARK 3 CHIRALITY : 0.099 501 REMARK 3 PLANARITY : 0.010 580 REMARK 3 DIHEDRAL : 6.912 470 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -68.1476 68.5294 -16.4088 REMARK 3 T TENSOR REMARK 3 T11: 0.2144 T22: 0.3013 REMARK 3 T33: 0.2137 T12: -0.0490 REMARK 3 T13: 0.0003 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 1.8168 L22: 1.1982 REMARK 3 L33: 0.9610 L12: 0.3203 REMARK 3 L13: -0.2616 L23: -0.1136 REMARK 3 S TENSOR REMARK 3 S11: 0.0152 S12: 0.2229 S13: -0.0239 REMARK 3 S21: -0.0319 S22: 0.0865 S23: -0.0430 REMARK 3 S31: -0.0719 S32: 0.1185 S33: -0.0811 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 7LW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255112. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6-6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0711 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54383 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 92.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 1.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6WKS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (V/V) PROPANOL-2, 0.1 M MES/NAOH REMARK 280 PH 6.0, 0.2 M CALCCIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.98700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.97400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.97400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 18.98700 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: 3880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 ALA B 1 REMARK 465 GLY B 2 REMARK 465 ASN B 3 REMARK 465 ALA B 4 REMARK 465 THR B 5 REMARK 465 GLU B 6 REMARK 465 VAL B 7 REMARK 465 PRO B 8 REMARK 465 ALA B 9 REMARK 465 ASN B 10 REMARK 465 SER B 11 REMARK 465 THR B 12 REMARK 465 VAL B 13 REMARK 465 LEU B 14 REMARK 465 SER B 15 REMARK 465 PHE B 16 REMARK 465 CYS B 17 REMARK 465 GLN B 132 REMARK 465 LEU B 133 REMARK 465 ARG B 134 REMARK 465 GLU B 135 REMARK 465 PRO B 136 REMARK 465 MET B 137 REMARK 465 LEU B 138 REMARK 465 GLN B 139 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 24 CG CD CE NZ REMARK 470 TYR A 30 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 LYS A 141 CG CD CE NZ REMARK 470 LYS A 253 CG CD CE NZ REMARK 470 LYS A 263 CG CD CE NZ REMARK 470 GLU A 264 CG CD OE1 OE2 REMARK 470 MET A 270 CG SD CE REMARK 470 ASN A 298 CG OD1 ND2 REMARK 470 GLN B 36 CG CD OE1 NE2 REMARK 470 ASP B 131 CG OD1 OD2 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 HZ3 LYS A 182 OXT ACT A 310 1.51 REMARK 500 O SER A 276 O HOH A 401 2.07 REMARK 500 O HOH A 401 O HOH A 484 2.08 REMARK 500 O HOH A 443 O HOH A 527 2.08 REMARK 500 O HOH A 508 O HOH A 526 2.15 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 A 25 CB CYS A 25 SG 0.142 REMARK 500 MET A 41 CG MET A 41 SD 0.159 REMARK 500 TYR A 47 CB TYR A 47 CG 0.097 REMARK 500 CYS A 51 CB CYS A 51 SG 0.155 REMARK 500 ASP A 114 CB ASP A 114 CG 0.153 REMARK 500 CYS A 115 CB CYS A 115 SG 0.108 REMARK 500 ASP A 125 CB ASP A 125 CG 0.137 REMARK 500 CYS A 154 CB CYS A 154 SG 0.149 REMARK 500 GLU A 173 CB GLU A 173 CG 0.132 REMARK 500 GLU A 173 CG GLU A 173 CD 0.116 REMARK 500 TRP A 190 CB TRP A 190 CG 0.118 REMARK 500 TRP A 190 CE3 TRP A 190 CZ3 0.111 REMARK 500 CYS A 209 CB CYS A 209 SG 0.152 REMARK 500 TRP A 231 CB TRP A 231 CG 0.128 REMARK 500 CYS B 41 CB CYS B 41 SG 0.196 REMARK 500 CYS B 46 CB CYS B 46 SG 0.121 REMARK 500 ASP B 64 CB ASP B 64 CG 0.134 REMARK 500 CYS B 73 CB CYS B 73 SG 0.167 REMARK 500 CYS B 74 CB CYS B 74 SG 0.142 REMARK 500 CYS B 77 CB CYS B 77 SG 0.113 REMARK 500 CYS B 103 CB CYS B 103 SG 0.106 REMARK 500 CYS B 117 CB CYS B 117 SG 0.115 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 19 CG - CD - NE ANGL. DEV. = -27.0 DEGREES REMARK 500 ARG A 19 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 MET A 41 CA - CB - CG ANGL. DEV. = 11.6 DEGREES REMARK 500 CYS A 51 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 102 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 179 CB - CG - OD2 ANGL. DEV. = -8.3 DEGREES REMARK 500 LEU A 206 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 ASP A 246 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 255 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 CYS B 41 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP B 64 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 CYS B 73 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 CYS B 74 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 CYS B 77 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG B 78 NE - CZ - NH1 ANGL. DEV. = 3.9 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 ASN A 29 -166.95 -73.95 REMARK 500 TYR A 30 100.41 119.11 REMARK 500 THR A 58 67.09 -101.41 REMARK 500 LYS A 135 4.76 -66.86 REMARK 500 GLU A 147 -114.06 -105.05 REMARK 500 ASN A 210 97.05 72.35 REMARK 500 ASN A 286 -153.73 -95.16 REMARK 500 ASN A 297 1.16 -155.21 REMARK 500 ASN B 62 -168.34 -105.88 REMARK 500 PRO B 86 -34.14 -39.86 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 ARG A 19 0.07 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 539 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 540 DISTANCE = 7.58 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 B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 74 SG REMARK 620 2 CYS B 77 SG 110.8 REMARK 620 3 HIS B 83 NE2 104.4 123.2 REMARK 620 4 CYS B 90 SG 103.3 114.1 98.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 117 SG REMARK 620 2 CYS B 120 SG 101.8 REMARK 620 3 CYS B 128 SG 108.3 100.8 REMARK 620 4 CYS B 130 SG 130.2 107.3 104.8 REMARK 620 N 1 2 3 DBREF 7LW4 A 1 298 UNP P0DTD1 R1AB_SARS2 6799 7096 DBREF 7LW4 B 1 139 UNP P0DTD1 R1AB_SARS2 4254 4392 SEQADV 7LW4 LYS A 138 UNP P0DTD1 ASN 6936 CONFLICT SEQRES 1 A 298 SER SER GLN ALA TRP GLN PRO GLY VAL ALA MET PRO ASN SEQRES 2 A 298 LEU TYR LYS MET GLN ARG MET LEU LEU GLU LYS CYS ASP SEQRES 3 A 298 LEU GLN ASN TYR GLY ASP SER ALA THR LEU PRO LYS GLY SEQRES 4 A 298 ILE MET MET ASN VAL ALA LYS TYR THR GLN LEU CYS GLN SEQRES 5 A 298 TYR LEU ASN THR LEU THR LEU ALA VAL PRO TYR ASN MET SEQRES 6 A 298 ARG VAL ILE HIS PHE GLY ALA GLY SER ASP LYS GLY VAL SEQRES 7 A 298 ALA PRO GLY THR ALA VAL LEU ARG GLN TRP LEU PRO THR SEQRES 8 A 298 GLY THR LEU LEU VAL ASP SER ASP LEU ASN ASP PHE VAL SEQRES 9 A 298 SER ASP ALA ASP SER THR LEU ILE GLY ASP CYS ALA THR SEQRES 10 A 298 VAL HIS THR ALA ASN LYS TRP ASP LEU ILE ILE SER ASP SEQRES 11 A 298 MET TYR ASP PRO LYS THR LYS LYS VAL THR LYS GLU ASN SEQRES 12 A 298 ASP SER LYS GLU GLY PHE PHE THR TYR ILE CYS GLY PHE SEQRES 13 A 298 ILE GLN GLN LYS LEU ALA LEU GLY GLY SER VAL ALA ILE SEQRES 14 A 298 LYS ILE THR GLU HIS SER TRP ASN ALA ASP LEU TYR LYS SEQRES 15 A 298 LEU MET GLY HIS PHE ALA TRP TRP THR ALA PHE VAL THR SEQRES 16 A 298 ASN VAL ASN ALA SER SER SER GLU ALA PHE LEU ILE GLY SEQRES 17 A 298 CYS ASN TYR LEU GLY LYS PRO ARG GLU GLN ILE ASP GLY SEQRES 18 A 298 TYR VAL MET HIS ALA ASN TYR ILE PHE TRP ARG ASN THR SEQRES 19 A 298 ASN PRO ILE GLN LEU SER SER TYR SER LEU PHE ASP MET SEQRES 20 A 298 SER LYS PHE PRO LEU LYS LEU ARG GLY THR ALA VAL MET SEQRES 21 A 298 SER LEU LYS GLU GLY GLN ILE ASN ASP MET ILE LEU SER SEQRES 22 A 298 LEU LEU SER LYS GLY ARG LEU ILE ILE ARG GLU ASN ASN SEQRES 23 A 298 ARG VAL VAL ILE SER SER ASP VAL LEU VAL ASN ASN SEQRES 1 B 139 ALA GLY ASN ALA THR GLU VAL PRO ALA ASN SER THR VAL SEQRES 2 B 139 LEU SER PHE CYS ALA PHE ALA VAL ASP ALA ALA LYS ALA SEQRES 3 B 139 TYR LYS ASP TYR LEU ALA SER GLY GLY GLN PRO ILE THR SEQRES 4 B 139 ASN CYS VAL LYS MET LEU CYS THR HIS THR GLY THR GLY SEQRES 5 B 139 GLN ALA ILE THR VAL THR PRO GLU ALA ASN MET ASP GLN SEQRES 6 B 139 GLU SER PHE GLY GLY ALA SER CYS CYS LEU TYR CYS ARG SEQRES 7 B 139 CYS HIS ILE ASP HIS PRO ASN PRO LYS GLY PHE CYS ASP SEQRES 8 B 139 LEU LYS GLY LYS TYR VAL GLN ILE PRO THR THR CYS ALA SEQRES 9 B 139 ASN ASP PRO VAL GLY PHE THR LEU LYS ASN THR VAL CYS SEQRES 10 B 139 THR VAL CYS GLY MET TRP LYS GLY TYR GLY CYS SER CYS SEQRES 11 B 139 ASP GLN LEU ARG GLU PRO MET LEU GLN HET MES A 301 25 HET ACT A 302 7 HET ACT A 303 7 HET EDO A 304 10 HET EDO A 305 10 HET ACT A 306 7 HET EDO A 307 10 HET ACT A 308 7 HET ACT A 309 7 HET ACT A 310 5 HET ACT A 311 7 HET SAH A 312 45 HET ACT A 313 4 HET ZN B 201 1 HET ZN B 202 1 HET ACT B 203 4 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 MES C6 H13 N O4 S FORMUL 4 ACT 9(C2 H3 O2 1-) FORMUL 6 EDO 3(C2 H6 O2) FORMUL 14 SAH C14 H20 N6 O5 S FORMUL 16 ZN 2(ZN 2+) FORMUL 19 HOH *165(H2 O) HELIX 1 AA1 SER A 1 GLN A 6 5 6 HELIX 2 AA2 MET A 41 ASN A 55 1 15 HELIX 3 AA3 ALA A 79 LEU A 89 1 11 HELIX 4 AA4 ASP A 114 ALA A 116 5 3 HELIX 5 AA5 ASP A 133 LYS A 137 5 5 HELIX 6 AA6 GLY A 148 LYS A 160 1 13 HELIX 7 AA7 ASN A 177 MET A 184 1 8 HELIX 8 AA8 ASP A 220 ASN A 235 1 16 HELIX 9 AA9 SER A 241 ASP A 246 5 6 HELIX 10 AB1 ASN A 268 LYS A 277 1 10 HELIX 11 AB2 ALA B 23 SER B 33 1 11 HELIX 12 AB3 ALA B 71 CYS B 73 5 3 HELIX 13 AB4 CYS B 74 HIS B 80 1 7 HELIX 14 AB5 THR B 102 ALA B 104 5 3 HELIX 15 AB6 ASP B 106 ASN B 114 1 9 SHEET 1 AA1 8 GLY A 8 ALA A 10 0 SHEET 2 AA1 8 PHE A 187 THR A 195 -1 O VAL A 194 N VAL A 9 SHEET 3 AA1 8 ALA A 204 TYR A 211 -1 O PHE A 205 N PHE A 193 SHEET 4 AA1 8 LEU A 161 ILE A 171 -1 N ILE A 171 O ALA A 204 SHEET 5 AA1 8 TRP A 124 SER A 129 1 N TRP A 124 O ALA A 162 SHEET 6 AA1 8 ARG A 66 PHE A 70 1 N PHE A 70 O ILE A 128 SHEET 7 AA1 8 LEU A 94 ASP A 99 1 O LEU A 94 N VAL A 67 SHEET 8 AA1 8 SER A 109 ILE A 112 1 O LEU A 111 N ASP A 97 SHEET 1 AA2 2 VAL A 118 THR A 120 0 SHEET 2 AA2 2 ILE A 290 SER A 292 -1 O SER A 291 N HIS A 119 SHEET 1 AA3 2 VAL A 259 MET A 260 0 SHEET 2 AA3 2 ILE A 281 ILE A 282 1 O ILE A 281 N MET A 260 SHEET 1 AA4 3 ILE B 55 THR B 56 0 SHEET 2 AA4 3 TYR B 96 PRO B 100 -1 O TYR B 96 N THR B 56 SHEET 3 AA4 3 GLN B 65 GLY B 69 -1 N GLU B 66 O ILE B 99 LINK SG CYS B 74 ZN ZN B 201 1555 1555 2.41 LINK SG CYS B 77 ZN ZN B 201 1555 1555 2.37 LINK NE2 HIS B 83 ZN ZN B 201 1555 1555 2.30 LINK SG CYS B 90 ZN ZN B 201 1555 1555 2.36 LINK SG CYS B 117 ZN ZN B 202 1555 1555 2.37 LINK SG CYS B 120 ZN ZN B 202 1555 1555 2.40 LINK SG CYS B 128 ZN ZN B 202 1555 1555 2.38 LINK SG CYS B 130 ZN ZN B 202 1555 1555 2.34 CRYST1 184.589 184.589 56.961 90.00 90.00 120.00 P 31 2 1 6 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 0.005417 0.003128 0.000000 0.00000 SCALE2 0.000000 0.006256 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017556 0.00000