HEADER HYDROLASE 31-MAR-21 7MBG TITLE SARS-COV-2 MAIN PROTEASE IN ORTHORHOMBIC SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; 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_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 KEYWDS 3CL, PROTEASE, SARS, SARS-COV-2, COVID, MAIN PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.FEARON,A.DOUANGAMATH,F.VON DELFT,G.D.NOSKE,A.M.NAKAMURA, AUTHOR 2 V.O.GAWRILJUK,G.M.A.LIMA,A.C.M.ZERI,A.F.Z.NASCIMENTO,G.OLIVA, AUTHOR 3 A.S.GODOY REVDAT 5 18-OCT-23 7MBG 1 REMARK REVDAT 4 28-JUL-21 7MBG 1 JRNL REVDAT 3 07-JUL-21 7MBG 1 JRNL REVDAT 2 21-APR-21 7MBG 1 AUTHOR REVDAT 1 07-APR-21 7MBG 0 JRNL AUTH G.D.NOSKE,A.M.NAKAMURA,V.O.GAWRILJUK,R.S.FERNANDES, JRNL AUTH 2 G.M.A.LIMA,H.V.D.ROSA,H.D.PEREIRA,A.C.M.ZERI, JRNL AUTH 3 A.F.Z.NASCIMENTO,M.C.L.C.FREIRE,D.FEARON,A.DOUANGAMATH, JRNL AUTH 4 F.VON DELFT,G.OLIVA,A.S.GODOY JRNL TITL A CRYSTALLOGRAPHIC SNAPSHOT OF SARS-COV-2 MAIN PROTEASE JRNL TITL 2 MATURATION PROCESS. JRNL REF J.MOL.BIOL. V. 433 67118 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 34174328 JRNL DOI 10.1016/J.JMB.2021.167118 REMARK 2 REMARK 2 RESOLUTION. 1.86 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 57213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2914 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 56.1900 - 5.1300 1.00 2787 152 0.1811 0.1790 REMARK 3 2 5.1300 - 4.0700 1.00 2665 157 0.1500 0.1800 REMARK 3 3 4.0700 - 3.5600 1.00 2605 172 0.1604 0.1874 REMARK 3 4 3.5600 - 3.2300 1.00 2637 134 0.1764 0.1917 REMARK 3 5 3.2300 - 3.0000 1.00 2622 133 0.1852 0.2560 REMARK 3 6 3.0000 - 2.8200 1.00 2604 130 0.1950 0.2410 REMARK 3 7 2.8200 - 2.6800 1.00 2605 134 0.1860 0.1907 REMARK 3 8 2.6800 - 2.5700 1.00 2589 124 0.1994 0.2324 REMARK 3 9 2.5700 - 2.4700 1.00 2593 131 0.1922 0.2607 REMARK 3 10 2.4700 - 2.3800 0.99 2552 138 0.2033 0.2721 REMARK 3 11 2.3800 - 2.3100 0.99 2553 168 0.2117 0.2500 REMARK 3 12 2.3100 - 2.2400 1.00 2534 148 0.2124 0.2501 REMARK 3 13 2.2400 - 2.1800 0.99 2592 114 0.2238 0.2556 REMARK 3 14 2.1800 - 2.1300 0.99 2568 137 0.2314 0.2416 REMARK 3 15 2.1300 - 2.0800 0.99 2535 142 0.2518 0.3315 REMARK 3 16 2.0800 - 2.0400 1.00 2534 128 0.2682 0.2520 REMARK 3 17 2.0400 - 2.0000 0.99 2599 126 0.2824 0.3229 REMARK 3 18 2.0000 - 1.9600 0.99 2523 137 0.2905 0.3030 REMARK 3 19 1.9600 - 1.9200 1.00 2549 128 0.3021 0.3312 REMARK 3 20 1.9200 - 1.8900 0.98 2506 143 0.3273 0.3804 REMARK 3 21 1.8900 - 1.8600 0.99 2547 138 0.3732 0.3921 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.00 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 : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1423 -6.6303 18.2511 REMARK 3 T TENSOR REMARK 3 T11: 0.2138 T22: 0.2218 REMARK 3 T33: 0.2016 T12: -0.0325 REMARK 3 T13: -0.0229 T23: -0.0197 REMARK 3 L TENSOR REMARK 3 L11: 1.2605 L22: 1.0073 REMARK 3 L33: 2.3745 L12: -0.4910 REMARK 3 L13: -0.8448 L23: -0.1302 REMARK 3 S TENSOR REMARK 3 S11: 0.0106 S12: -0.0228 S13: 0.0992 REMARK 3 S21: -0.0800 S22: 0.0192 S23: 0.0328 REMARK 3 S31: 0.0454 S32: -0.1894 S33: -0.0225 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.2662 -1.0978 29.8539 REMARK 3 T TENSOR REMARK 3 T11: 0.2591 T22: 0.4520 REMARK 3 T33: 0.3333 T12: 0.0319 REMARK 3 T13: -0.0055 T23: -0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.2201 L22: 0.3651 REMARK 3 L33: 3.3133 L12: 0.4436 REMARK 3 L13: 1.0582 L23: 0.7932 REMARK 3 S TENSOR REMARK 3 S11: -0.0268 S12: 0.4745 S13: 0.2815 REMARK 3 S21: -0.2331 S22: -0.0362 S23: 0.1017 REMARK 3 S31: -0.1869 S32: -0.1757 S33: 0.0120 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 139 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.4666 -8.2987 21.3453 REMARK 3 T TENSOR REMARK 3 T11: 0.2025 T22: 0.2289 REMARK 3 T33: 0.1827 T12: -0.0096 REMARK 3 T13: -0.0008 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 2.4199 L22: 1.2013 REMARK 3 L33: 1.5211 L12: 0.3626 REMARK 3 L13: -0.1288 L23: -0.2475 REMARK 3 S TENSOR REMARK 3 S11: -0.0263 S12: 0.0690 S13: 0.0631 REMARK 3 S21: -0.0838 S22: -0.0189 S23: 0.0531 REMARK 3 S31: 0.0606 S32: -0.2929 S33: 0.0321 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 140 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.2385 -7.2144 19.9780 REMARK 3 T TENSOR REMARK 3 T11: 0.2694 T22: 0.3197 REMARK 3 T33: 0.2512 T12: -0.0201 REMARK 3 T13: -0.0190 T23: -0.0543 REMARK 3 L TENSOR REMARK 3 L11: 3.5233 L22: 0.5621 REMARK 3 L33: 4.2204 L12: 0.9971 REMARK 3 L13: 0.2750 L23: 0.0356 REMARK 3 S TENSOR REMARK 3 S11: 0.0102 S12: 0.4076 S13: -0.0280 REMARK 3 S21: 0.1648 S22: 0.0007 S23: -0.2036 REMARK 3 S31: 0.4213 S32: 0.1451 S33: 0.0612 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.7290 -2.5211 32.1688 REMARK 3 T TENSOR REMARK 3 T11: 0.1755 T22: 0.2580 REMARK 3 T33: 0.2054 T12: 0.0013 REMARK 3 T13: -0.0070 T23: -0.0327 REMARK 3 L TENSOR REMARK 3 L11: 1.5375 L22: 0.3842 REMARK 3 L33: 1.0471 L12: -0.0969 REMARK 3 L13: -0.0809 L23: -0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.0147 S12: -0.2792 S13: 0.2163 REMARK 3 S21: 0.0866 S22: 0.0342 S23: -0.1261 REMARK 3 S31: -0.0436 S32: -0.0623 S33: -0.0304 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 201 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.2087 -7.0123 33.1106 REMARK 3 T TENSOR REMARK 3 T11: 0.1798 T22: 0.1932 REMARK 3 T33: 0.2563 T12: 0.0010 REMARK 3 T13: -0.0222 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 3.1256 L22: 1.7269 REMARK 3 L33: 2.3441 L12: 0.5273 REMARK 3 L13: -0.1004 L23: 0.1515 REMARK 3 S TENSOR REMARK 3 S11: -0.0188 S12: 0.0149 S13: 0.0862 REMARK 3 S21: -0.0317 S22: 0.0415 S23: -0.0819 REMARK 3 S31: -0.0608 S32: 0.1010 S33: -0.0139 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8907 -14.9357 -2.9747 REMARK 3 T TENSOR REMARK 3 T11: 0.3510 T22: 0.3204 REMARK 3 T33: 0.3560 T12: 0.0626 REMARK 3 T13: 0.0561 T23: -0.0355 REMARK 3 L TENSOR REMARK 3 L11: 1.6639 L22: 2.4039 REMARK 3 L33: 2.8641 L12: 0.1433 REMARK 3 L13: 0.7121 L23: 0.6758 REMARK 3 S TENSOR REMARK 3 S11: 0.1211 S12: 0.3667 S13: -0.2463 REMARK 3 S21: -0.2297 S22: 0.0258 S23: -0.4065 REMARK 3 S31: 0.4349 S32: 0.5248 S33: -0.0746 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 77 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.8723 -5.3346 0.7919 REMARK 3 T TENSOR REMARK 3 T11: 0.2181 T22: 0.2040 REMARK 3 T33: 0.2281 T12: 0.0294 REMARK 3 T13: 0.0439 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.8401 L22: 1.4454 REMARK 3 L33: 2.6100 L12: 1.1369 REMARK 3 L13: 0.4130 L23: 0.5568 REMARK 3 S TENSOR REMARK 3 S11: -0.0003 S12: 0.1012 S13: -0.0825 REMARK 3 S21: -0.0825 S22: -0.0206 S23: -0.1566 REMARK 3 S31: 0.0336 S32: 0.2203 S33: 0.0099 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 181 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6658 6.5619 7.8202 REMARK 3 T TENSOR REMARK 3 T11: 0.2295 T22: 0.2570 REMARK 3 T33: 0.2882 T12: -0.0041 REMARK 3 T13: 0.0275 T23: 0.0215 REMARK 3 L TENSOR REMARK 3 L11: 1.5100 L22: 1.1283 REMARK 3 L33: 2.9736 L12: 0.4850 REMARK 3 L13: -0.2891 L23: 1.3516 REMARK 3 S TENSOR REMARK 3 S11: -0.0962 S12: -0.1007 S13: -0.0490 REMARK 3 S21: -0.0314 S22: 0.3054 S23: -0.3623 REMARK 3 S31: -0.0762 S32: 0.6919 S33: -0.1697 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 214 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 3.3833 18.9505 16.6582 REMARK 3 T TENSOR REMARK 3 T11: 0.2564 T22: 0.1689 REMARK 3 T33: 0.1807 T12: 0.0032 REMARK 3 T13: -0.0038 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 2.0002 L22: 3.8452 REMARK 3 L33: 2.7214 L12: 0.2057 REMARK 3 L13: -0.4254 L23: 1.0027 REMARK 3 S TENSOR REMARK 3 S11: -0.0337 S12: -0.0151 S13: -0.0801 REMARK 3 S21: -0.1789 S22: -0.0042 S23: -0.1264 REMARK 3 S31: -0.1908 S32: -0.0066 S33: 0.0331 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 7MBG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000255882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9120 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57312 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 67.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.17600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 3.08400 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 5RGQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.7, 5% V/V DMSO, 8% W/V REMARK 280 PEG4000, 30% W/V PEG400, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 33.62500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.13000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.08000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.13000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.62500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.08000 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: 6320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 18.0 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 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 THR B 45 REMARK 465 SER B 46 REMARK 465 GLU B 47 REMARK 465 GLN B 306 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 OD1 ASP B 263 O HOH B 501 1.93 REMARK 500 OD1 ASP A 56 O HOH A 501 2.00 REMARK 500 N GLN B 192 O HOH B 502 2.01 REMARK 500 NE2 GLN A 273 O HOH A 502 2.05 REMARK 500 OD2 ASP A 216 O HOH A 503 2.08 REMARK 500 OG SER A 1 O HOH A 504 2.08 REMARK 500 O DMS B 403 O HOH B 503 2.09 REMARK 500 O HOH A 595 O HOH A 700 2.11 REMARK 500 OD1 ASP B 92 O HOH B 504 2.12 REMARK 500 OD2 ASP A 34 O HOH A 505 2.14 REMARK 500 O ARG B 60 O HOH B 505 2.17 REMARK 500 O LEU B 75 O HOH B 506 2.18 REMARK 500 O CYS B 300 O HOH B 507 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 A 128 CB CYS A 128 SG -0.133 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 LEU B 67 CB - CG - CD2 ANGL. DEV. = 16.5 DEGREES REMARK 500 GLU B 270 CA - C - O ANGL. DEV. = 12.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 33 -129.54 52.76 REMARK 500 ASP A 48 35.96 -92.18 REMARK 500 ASN A 84 -117.13 47.47 REMARK 500 TYR A 154 -95.46 51.26 REMARK 500 ASP B 33 -128.40 47.61 REMARK 500 MET B 49 92.32 -30.21 REMARK 500 LEU B 50 40.26 -75.58 REMARK 500 ASN B 51 65.07 -168.84 REMARK 500 ASN B 84 -126.69 53.56 REMARK 500 TYR B 154 -114.20 67.08 REMARK 500 THR B 225 -169.73 -126.58 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 B 638 DISTANCE = 7.29 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 407 DBREF 7MBG A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7MBG B 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 SEQRES 1 B 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 B 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 B 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 B 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 B 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 B 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 B 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 B 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 B 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 B 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 B 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 B 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 B 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 B 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 B 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 B 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 B 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 B 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 B 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 B 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 B 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 B 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 B 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 B 306 CYS SER GLY VAL THR PHE GLN HET DMS A 401 4 HET DMS A 402 4 HET DMS A 403 4 HET DMS A 404 4 HET DMS A 405 4 HET DMS A 406 4 HET DMS A 407 4 HET DMS B 401 4 HET DMS B 402 4 HET DMS B 403 4 HET DMS B 404 4 HET DMS B 405 4 HET DMS B 406 4 HET DMS B 407 4 HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 DMS 14(C2 H6 O S) FORMUL 17 HOH *353(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 ARG A 60 1 8 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 LYS A 236 1 11 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 GLY A 275 1 16 HELIX 10 AB1 THR A 292 GLY A 302 1 11 HELIX 11 AB2 SER B 10 GLY B 15 1 6 HELIX 12 AB3 HIS B 41 ILE B 43 5 3 HELIX 13 AB4 ASN B 53 ARG B 60 1 8 HELIX 14 AB5 SER B 62 PHE B 66 5 5 HELIX 15 AB6 ILE B 200 ASN B 214 1 15 HELIX 16 AB7 THR B 226 TYR B 237 1 12 HELIX 17 AB8 THR B 243 LEU B 250 1 8 HELIX 18 AB9 LEU B 250 GLY B 258 1 9 HELIX 19 AC1 ALA B 260 GLY B 275 1 16 HELIX 20 AC2 THR B 292 CYS B 300 1 9 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88 SHEET 1 AA2 5 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASP A 153 O CYS A 156 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA3 3 TYR A 101 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 LEU B 67 ALA B 70 -1 N ALA B 70 O VAL B 73 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O GLY B 29 N VAL B 18 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N SER B 81 O LYS B 88 SHEET 1 AA5 5 TYR B 101 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114 SHEET 1 AA6 3 TYR B 101 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 SITE 1 AC1 7 MET A 6 ARG A 298 GLN A 299 DMS A 404 SITE 2 AC1 7 TYR B 118 SER B 123 HOH B 531 SITE 1 AC2 4 GLY A 15 MET A 17 LYS A 97 HOH A 510 SITE 1 AC3 6 MET A 165 GLU A 166 PRO A 168 GLN A 189 SITE 2 AC3 6 THR A 190 GLN A 192 SITE 1 AC4 5 MET A 6 ALA A 7 GLN A 127 ARG A 298 SITE 2 AC4 5 DMS A 401 SITE 1 AC5 4 LEU A 141 SER A 144 HIS A 163 GLU A 166 SITE 1 AC6 4 HIS A 41 TYR A 54 ASP A 187 GLN A 189 SITE 1 AC7 8 GLN A 19 GLN A 69 ALA A 70 GLY A 71 SITE 2 AC7 8 ASN A 119 GLY A 120 SER A 121 HOH A 510 SITE 1 AC8 5 MET B 6 GLN B 127 ASP B 295 ARG B 298 SITE 2 AC8 5 HOH B 557 SITE 1 AC9 3 PHE B 3 ARG B 4 LEU B 282 SITE 1 AD1 6 PRO A 184 VAL A 186 ARG A 188 LYS B 100 SITE 2 AD1 6 TYR B 101 HOH B 503 SITE 1 AD2 7 PHE B 140 LEU B 141 ASN B 142 SER B 144 SITE 2 AD2 7 HIS B 163 MET B 165 GLU B 166 SITE 1 AD3 4 ALA B 70 VAL B 73 PRO B 96 HOH B 569 SITE 1 AD4 3 VAL B 212 THR B 257 HOH B 560 SITE 1 AD5 4 MET B 165 ASP B 187 ARG B 188 GLN B 189 CRYST1 67.250 98.160 102.260 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014870 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009779 0.00000