HEADER VIRAL PROTEIN 26-JUN-20 6XKM TITLE ROOM TEMPERATURE STRUCTURE OF SARS-COV-2 NSP10/NSP16 METHYLTRANSFERASE TITLE 2 IN A COMPLEX WITH SAM DETERMINED BY FIXED-TARGET SERIAL TITLE 3 CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2'-O-METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 16; 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 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VARIANT: MAGIC; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PMCSG53; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 15 2; SOURCE 16 ORGANISM_COMMON: 2019-NCOV; SOURCE 17 ORGANISM_TAXID: 2697049; SOURCE 18 GENE: REP, 1A-1B; SOURCE 19 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 21 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 22 EXPRESSION_SYSTEM_VARIANT: MAGIC KEYWDS SARS COV-2, SERIAL CRYSTALLOGRAPHY, METHYLTRANSFERASE, S- KEYWDS 2 ADENOSYLMETHIONINE, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS OF INFECTIOUS DISEASES, CSGID, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.WILAMOWSKI,D.A.SHERRELL,G.MINASOV,Y.KIM,L.SHUVALOVA,A.LAVENS, AUTHOR 2 R.CHARD,M.ROSAS-LEMUS,N.MALTSEVA,R.JEDRZEJCZAK,K.MICHALSKA, AUTHOR 3 K.J.F.SATCHELL,A.JOACHIMIAK,CENTER FOR STRUCTURAL GENOMICS OF AUTHOR 4 INFECTIOUS DISEASES (CSGID) REVDAT 4 18-OCT-23 6XKM 1 REMARK REVDAT 3 28-JUL-21 6XKM 1 JRNL REVDAT 2 26-AUG-20 6XKM 1 REMARK DBREF SEQADV HELIX REVDAT 2 2 1 SHEET LINK SITE ATOM REVDAT 1 08-JUL-20 6XKM 0 JRNL AUTH M.WILAMOWSKI,D.A.SHERRELL,G.MINASOV,Y.KIM,L.SHUVALOVA, JRNL AUTH 2 A.LAVENS,R.CHARD,N.MALTSEVA,R.JEDRZEJCZAK,M.ROSAS-LEMUS, JRNL AUTH 3 N.SAINT,I.T.FOSTER,K.MICHALSKA,K.J.F.SATCHELL,A.JOACHIMIAK JRNL TITL 2'-O METHYLATION OF RNA CAP IN SARS-COV-2 CAPTURED BY SERIAL JRNL TITL 2 CRYSTALLOGRAPHY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33972410 JRNL DOI 10.1073/PNAS.2100170118 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 39686 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2054 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2893 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3630 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3188 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : 0.94000 REMARK 3 B12 (A**2) : -0.15000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.214 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.500 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3313 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3000 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4497 ; 1.217 ; 1.643 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6991 ; 0.323 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 2.980 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;27.727 ;23.973 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 555 ; 9.938 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ; 7.562 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 440 ; 0.049 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3695 ; 0.053 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 658 ; 0.049 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6799 A 6826 REMARK 3 ORIGIN FOR THE GROUP (A): -70.7947 46.5368 -7.3174 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.2009 REMARK 3 T33: 0.1712 T12: -0.0678 REMARK 3 T13: -0.0472 T23: -0.0576 REMARK 3 L TENSOR REMARK 3 L11: 3.3589 L22: 5.0485 REMARK 3 L33: 3.8176 L12: -1.5354 REMARK 3 L13: -0.6843 L23: 2.3366 REMARK 3 S TENSOR REMARK 3 S11: -0.0244 S12: 0.2455 S13: -0.6351 REMARK 3 S21: -0.2829 S22: -0.0897 S23: 0.6540 REMARK 3 S31: 0.1660 S32: -0.2573 S33: 0.1141 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6827 A 6916 REMARK 3 ORIGIN FOR THE GROUP (A): -61.6229 63.5972 7.8041 REMARK 3 T TENSOR REMARK 3 T11: 0.1270 T22: 0.1341 REMARK 3 T33: 0.0183 T12: -0.0632 REMARK 3 T13: 0.0075 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 3.2569 L22: 2.1662 REMARK 3 L33: 1.7789 L12: 0.2878 REMARK 3 L13: 0.1441 L23: 0.2096 REMARK 3 S TENSOR REMARK 3 S11: -0.0357 S12: -0.1542 S13: 0.2118 REMARK 3 S21: 0.1472 S22: 0.0499 S23: -0.0507 REMARK 3 S31: -0.1044 S32: 0.0853 S33: -0.0143 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6917 A 7050 REMARK 3 ORIGIN FOR THE GROUP (A): -59.8315 52.4191 -1.2321 REMARK 3 T TENSOR REMARK 3 T11: 0.0990 T22: 0.1389 REMARK 3 T33: 0.0334 T12: -0.0435 REMARK 3 T13: -0.0095 T23: -0.0356 REMARK 3 L TENSOR REMARK 3 L11: 1.6376 L22: 2.4336 REMARK 3 L33: 2.5623 L12: 0.0801 REMARK 3 L13: -0.0510 L23: 0.5895 REMARK 3 S TENSOR REMARK 3 S11: 0.0628 S12: 0.1646 S13: -0.2209 REMARK 3 S21: -0.0783 S22: 0.0055 S23: -0.0584 REMARK 3 S31: 0.0753 S32: 0.1822 S33: -0.0682 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7051 A 7096 REMARK 3 ORIGIN FOR THE GROUP (A): -49.2323 49.4454 16.1235 REMARK 3 T TENSOR REMARK 3 T11: 0.1271 T22: 0.1955 REMARK 3 T33: 0.0867 T12: 0.0274 REMARK 3 T13: -0.0697 T23: 0.0283 REMARK 3 L TENSOR REMARK 3 L11: 3.8843 L22: 6.2143 REMARK 3 L33: 4.0554 L12: 2.5096 REMARK 3 L13: -0.6089 L23: -2.4261 REMARK 3 S TENSOR REMARK 3 S11: 0.1247 S12: -0.3884 S13: -0.4915 REMARK 3 S21: 0.4042 S22: -0.0434 S23: -0.4833 REMARK 3 S31: 0.3378 S32: 0.1773 S33: -0.0814 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4271 B 4286 REMARK 3 ORIGIN FOR THE GROUP (A): -60.0467 95.6212 11.3526 REMARK 3 T TENSOR REMARK 3 T11: 0.4262 T22: 0.2517 REMARK 3 T33: 0.6644 T12: -0.0869 REMARK 3 T13: -0.0165 T23: -0.1742 REMARK 3 L TENSOR REMARK 3 L11: 8.2544 L22: 4.4917 REMARK 3 L33: 1.2792 L12: 5.3377 REMARK 3 L13: -2.5653 L23: -2.3282 REMARK 3 S TENSOR REMARK 3 S11: 0.2720 S12: -0.7164 S13: 0.4166 REMARK 3 S21: 0.2999 S22: -0.2811 S23: -0.0185 REMARK 3 S31: -0.2900 S32: 0.1725 S33: 0.0091 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4287 B 4332 REMARK 3 ORIGIN FOR THE GROUP (A): -69.7641 76.5062 14.3994 REMARK 3 T TENSOR REMARK 3 T11: 0.1643 T22: 0.1637 REMARK 3 T33: 0.1013 T12: -0.0148 REMARK 3 T13: 0.0493 T23: -0.0961 REMARK 3 L TENSOR REMARK 3 L11: 5.9199 L22: 2.9738 REMARK 3 L33: 2.0006 L12: 1.1375 REMARK 3 L13: -0.7544 L23: -0.1556 REMARK 3 S TENSOR REMARK 3 S11: -0.0013 S12: -0.4407 S13: 0.5899 REMARK 3 S21: 0.2419 S22: 0.0904 S23: 0.2197 REMARK 3 S31: -0.2818 S32: -0.1600 S33: -0.0891 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4333 B 4344 REMARK 3 ORIGIN FOR THE GROUP (A): -52.5847 83.0582 18.4732 REMARK 3 T TENSOR REMARK 3 T11: 0.1472 T22: 0.1363 REMARK 3 T33: 0.2810 T12: -0.0379 REMARK 3 T13: -0.0426 T23: -0.1347 REMARK 3 L TENSOR REMARK 3 L11: 9.4486 L22: 6.8791 REMARK 3 L33: 7.2555 L12: 2.5097 REMARK 3 L13: 6.3457 L23: -2.6188 REMARK 3 S TENSOR REMARK 3 S11: 0.2757 S12: 0.0184 S13: -0.0436 REMARK 3 S21: 0.2178 S22: -0.3791 S23: -0.2658 REMARK 3 S31: 0.1146 S32: 0.2931 S33: 0.1034 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4345 B 4385 REMARK 3 ORIGIN FOR THE GROUP (A): -70.5638 82.3708 21.3604 REMARK 3 T TENSOR REMARK 3 T11: 0.2750 T22: 0.1934 REMARK 3 T33: 0.2298 T12: -0.0803 REMARK 3 T13: 0.0842 T23: -0.1851 REMARK 3 L TENSOR REMARK 3 L11: 4.0820 L22: 2.7942 REMARK 3 L33: 6.0358 L12: -0.1728 REMARK 3 L13: -1.0486 L23: 0.0887 REMARK 3 S TENSOR REMARK 3 S11: 0.1248 S12: -0.6075 S13: 0.8848 REMARK 3 S21: 0.4161 S22: -0.0238 S23: 0.1557 REMARK 3 S31: -0.7236 S32: -0.1359 S33: -0.1010 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6XKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000250301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : SAGITTALLY FOCUSING MONO AND REMARK 200 VERTICALLY FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41770 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 49.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 82.41 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.24 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.580 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6W4H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 4.0 MG/ML (NSP10/NSP16 1:1), REMARK 280 0.15 M NACL, 0.01 M TRIS-HCL, 2 MM SAM, 1 MM TCEP, 5% GLYCEROL, REMARK 280 PH 7.5. PRECIPITATION BUFFER: 0.1 M MES PH 6.5, 0.9 M NAF. BATCH REMARK 280 CRYSTALLIZATION: 100 UL OF PROTEIN MIXED WITH 100 UL OF REMARK 280 PRECIPITATION BUFFER IN 500 UL POLYPROPYLENE TUBE., BATCH MODE, REMARK 280 TEMPERATURE 295K 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 17.54367 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 35.08733 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 35.08733 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 17.54367 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: 1950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 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 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 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 TYR A 30 126.84 -27.07 REMARK 500 GLU A 147 -112.81 -108.90 REMARK 500 ASN A 210 91.97 70.82 REMARK 500 ALA B 20 134.14 -177.59 REMARK 500 ASN B 62 -169.07 -103.87 REMARK 500 ASN B 62 -167.39 -103.87 REMARK 500 ASN B 62 -167.74 -103.87 REMARK 500 PRO B 84 33.32 -77.33 REMARK 500 PRO B 86 -38.65 -38.95 REMARK 500 ASP B 106 67.87 -155.04 REMARK 500 ASP B 131 55.50 -105.83 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 A7309 DISTANCE = 5.88 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 B4401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 74 SG REMARK 620 2 CYS B 77 SG 111.4 REMARK 620 3 HIS B 83 NE2 106.3 105.5 REMARK 620 4 CYS B 90 SG 113.7 115.1 103.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B4402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 117 SG REMARK 620 2 CYS B 120 SG 111.5 REMARK 620 3 CYS B 128 SG 89.9 116.9 REMARK 620 4 CYS B 130 SG 125.4 98.4 116.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 7101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 7102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 4401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 4402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6W4H RELATED DB: PDB REMARK 900 RELATED ID: 6WJT RELATED DB: PDB REMARK 900 RELATED ID: 6WKQ RELATED DB: PDB REMARK 900 RELATED ID: 6WQ3 RELATED DB: PDB REMARK 900 RELATED ID: 6WVN RELATED DB: PDB REMARK 900 RELATED ID: 6WRZ RELATED DB: PDB DBREF 6XKM A 1 298 UNP P0DTD1 R1AB_SARS2 6799 7096 DBREF 6XKM B 1 139 UNP P0DTD1 R1AB_SARS2 4254 4392 SEQADV 6XKM SER A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 6XKM ASN A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 6XKM ALA A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 6XKM SER B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 6XKM ASN B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 6XKM ALA B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 301 SER ASN ALA SER SER GLN ALA TRP GLN PRO GLY VAL ALA SEQRES 2 A 301 MET PRO ASN LEU TYR LYS MET GLN ARG MET LEU LEU GLU SEQRES 3 A 301 LYS CYS ASP LEU GLN ASN TYR GLY ASP SER ALA THR LEU SEQRES 4 A 301 PRO LYS GLY ILE MET MET ASN VAL ALA LYS TYR THR GLN SEQRES 5 A 301 LEU CYS GLN TYR LEU ASN THR LEU THR LEU ALA VAL PRO SEQRES 6 A 301 TYR ASN MET ARG VAL ILE HIS PHE GLY ALA GLY SER ASP SEQRES 7 A 301 LYS GLY VAL ALA PRO GLY THR ALA VAL LEU ARG GLN TRP SEQRES 8 A 301 LEU PRO THR GLY THR LEU LEU VAL ASP SER ASP LEU ASN SEQRES 9 A 301 ASP PHE VAL SER ASP ALA ASP SER THR LEU ILE GLY ASP SEQRES 10 A 301 CYS ALA THR VAL HIS THR ALA ASN LYS TRP ASP LEU ILE SEQRES 11 A 301 ILE SER ASP MET TYR ASP PRO LYS THR LYS ASN VAL THR SEQRES 12 A 301 LYS GLU ASN ASP SER LYS GLU GLY PHE PHE THR TYR ILE SEQRES 13 A 301 CYS GLY PHE ILE GLN GLN LYS LEU ALA LEU GLY GLY SER SEQRES 14 A 301 VAL ALA ILE LYS ILE THR GLU HIS SER TRP ASN ALA ASP SEQRES 15 A 301 LEU TYR LYS LEU MET GLY HIS PHE ALA TRP TRP THR ALA SEQRES 16 A 301 PHE VAL THR ASN VAL ASN ALA SER SER SER GLU ALA PHE SEQRES 17 A 301 LEU ILE GLY CYS ASN TYR LEU GLY LYS PRO ARG GLU GLN SEQRES 18 A 301 ILE ASP GLY TYR VAL MET HIS ALA ASN TYR ILE PHE TRP SEQRES 19 A 301 ARG ASN THR ASN PRO ILE GLN LEU SER SER TYR SER LEU SEQRES 20 A 301 PHE ASP MET SER LYS PHE PRO LEU LYS LEU ARG GLY THR SEQRES 21 A 301 ALA VAL MET SER LEU LYS GLU GLY GLN ILE ASN ASP MET SEQRES 22 A 301 ILE LEU SER LEU LEU SER LYS GLY ARG LEU ILE ILE ARG SEQRES 23 A 301 GLU ASN ASN ARG VAL VAL ILE SER SER ASP VAL LEU VAL SEQRES 24 A 301 ASN ASN SEQRES 1 B 142 SER ASN ALA ALA GLY ASN ALA THR GLU VAL PRO ALA ASN SEQRES 2 B 142 SER THR VAL LEU SER PHE CYS ALA PHE ALA VAL ASP ALA SEQRES 3 B 142 ALA LYS ALA TYR LYS ASP TYR LEU ALA SER GLY GLY GLN SEQRES 4 B 142 PRO ILE THR ASN CYS VAL LYS MET LEU CYS THR HIS THR SEQRES 5 B 142 GLY THR GLY GLN ALA ILE THR VAL THR PRO GLU ALA ASN SEQRES 6 B 142 MET ASP GLN GLU SER PHE GLY GLY ALA SER CYS CYS LEU SEQRES 7 B 142 TYR CYS ARG CYS HIS ILE ASP HIS PRO ASN PRO LYS GLY SEQRES 8 B 142 PHE CYS ASP LEU LYS GLY LYS TYR VAL GLN ILE PRO THR SEQRES 9 B 142 THR CYS ALA ASN ASP PRO VAL GLY PHE THR LEU LYS ASN SEQRES 10 B 142 THR VAL CYS THR VAL CYS GLY MET TRP LYS GLY TYR GLY SEQRES 11 B 142 CYS SER CYS ASP GLN LEU ARG GLU PRO MET LEU GLN HET CL A7101 1 HET SAM A7102 27 HET ZN B4401 1 HET ZN B4402 1 HETNAM CL CHLORIDE ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM ZN ZINC ION FORMUL 3 CL CL 1- FORMUL 4 SAM C15 H22 N6 O5 S FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *128(H2 O) HELIX 1 AA1 SER A 1 GLN A 6 5 6 HELIX 2 AA2 PRO A 12 MET A 17 1 6 HELIX 3 AA3 MET A 41 ASN A 55 1 15 HELIX 4 AA4 ALA A 79 LEU A 89 1 11 HELIX 5 AA5 ASP A 114 ALA A 116 5 3 HELIX 6 AA6 ASP A 133 LYS A 137 5 5 HELIX 7 AA7 GLY A 148 LYS A 160 1 13 HELIX 8 AA8 ASN A 177 MET A 184 1 8 HELIX 9 AA9 VAL A 197 ALA A 199 5 3 HELIX 10 AB1 ASP A 220 ASN A 235 1 16 HELIX 11 AB2 SER A 241 ASP A 246 5 6 HELIX 12 AB3 LYS A 263 ILE A 267 5 5 HELIX 13 AB4 ASN A 268 LYS A 277 1 10 HELIX 14 AB5 ASP B 22 SER B 33 1 12 HELIX 15 AB6 ALA B 71 CYS B 73 5 3 HELIX 16 AB7 CYS B 74 HIS B 80 1 7 HELIX 17 AB8 THR B 102 ALA B 104 5 3 HELIX 18 AB9 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 CYS A 209 N TRP A 189 SHEET 4 AA1 8 LEU A 161 ILE A 171 -1 N ILE A 169 O LEU A 206 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 SER A 109 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 ALA A 258 MET A 260 0 SHEET 2 AA3 2 LEU A 280 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 B4401 1555 1555 2.31 LINK SG CYS B 77 ZN ZN B4401 1555 1555 2.34 LINK NE2 HIS B 83 ZN ZN B4401 1555 1555 2.12 LINK SG CYS B 90 ZN ZN B4401 1555 1555 2.33 LINK SG CYS B 117 ZN ZN B4402 1555 1555 2.34 LINK SG CYS B 120 ZN ZN B4402 1555 1555 2.35 LINK SG CYS B 128 ZN ZN B4402 1555 1555 2.36 LINK SG CYS B 130 ZN ZN B4402 1555 1555 2.36 SITE 1 AC1 3 TYR A 132 THR A 172 HIS A 174 SITE 1 AC2 18 ASN A 43 TYR A 47 GLY A 71 GLY A 73 SITE 2 AC2 18 SER A 74 PRO A 80 GLY A 81 ASP A 99 SITE 3 AC2 18 LEU A 100 ASN A 101 ASP A 114 CYS A 115 SITE 4 AC2 18 ASP A 130 MET A 131 TYR A 132 HOH A7225 SITE 5 AC2 18 HOH A7230 HOH A7250 SITE 1 AC3 4 CYS B 74 CYS B 77 HIS B 83 CYS B 90 SITE 1 AC4 5 CYS B 117 VAL B 119 CYS B 120 CYS B 128 SITE 2 AC4 5 CYS B 130 CRYST1 170.410 170.410 52.631 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 0.005868 0.003388 0.000000 0.00000 SCALE2 0.000000 0.006776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019000 0.00000