HEADER VIRAL PROTEIN 29-SEP-20 7K9P TITLE ROOM TEMPERATURE STRUCTURE OF NSP15 ENDORIBONUCLEASE FROM SARS COV-2 TITLE 2 SOLVED USING SFX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDYLATE-SPECIFIC ENDORIBONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 15,NSP15; COMPND 5 EC: 3.1.-.-; COMPND 6 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-GOLD (DE3) KEYWDS SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS 2, ROOM TEMPERATURE KEYWDS 2 STRUCTURE, SERIAL FEMTOSECOND CRYSTALLOGRAPHY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.BOTHA,R.JERNIGAN,J.CHEN,M.A.COLEMAN,M.FRANK,T.D.GRANT,D.T.HANSEN, AUTHOR 2 G.KETAWALA,D.LOGESWARAN,J.MARTIN-GARCIA,N.NAGARATNAM,A.L.L.X.RAJ, AUTHOR 3 M.SHELBY,J.-H.YANG,M.C.YUNG,P.FROMME REVDAT 3 25-OCT-23 7K9P 1 REMARK REVDAT 2 08-FEB-23 7K9P 1 JRNL REVDAT 1 21-OCT-20 7K9P 0 JRNL AUTH R.J.JERNIGAN,D.LOGESWARAN,D.DOPPLER,N.NAGARATNAM,M.SONKER, JRNL AUTH 2 J.H.YANG,G.KETAWALA,J.M.MARTIN-GARCIA,M.L.SHELBY,T.D.GRANT, JRNL AUTH 3 V.MARIANI,A.TOLSTIKOVA,M.Z.SHEIKH,M.C.YUNG,M.A.COLEMAN, JRNL AUTH 4 S.ZAARE,E.K.KASCHNER,M.T.RABBANI,R.NAZARI,M.A.ZACKS,B.HAYES, JRNL AUTH 5 R.G.SIERRA,M.S.HUNTER,S.LISOVA,A.BATYUK,C.KUPITZ,S.BOUTET, JRNL AUTH 6 D.T.HANSEN,R.A.KIRIAN,M.SCHMIDT,R.FROMME,M.FRANK,A.ROS, JRNL AUTH 7 J.J.CHEN,S.BOTHA,P.FROMME JRNL TITL ROOM-TEMPERATURE STRUCTURAL STUDIES OF SARS-COV-2 PROTEIN JRNL TITL 2 NENDOU WITH AN X-RAY FREE-ELECTRON LASER. JRNL REF STRUCTURE 2022 JRNL REFN ISSN 0969-2126 JRNL PMID 36630960 JRNL DOI 10.1016/J.STR.2022.12.009 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 45981 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 2503 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3372 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 191 REMARK 3 BIN FREE R VALUE : 0.2990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5504 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.54000 REMARK 3 B22 (A**2) : -8.54000 REMARK 3 B33 (A**2) : 17.07000 REMARK 3 B12 (A**2) : 0.00000 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.183 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5644 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5243 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7657 ; 1.034 ; 1.884 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12202 ; 0.909 ; 2.934 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 694 ; 5.347 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 257 ;35.260 ;25.331 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 980 ;14.785 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;13.657 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 873 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6238 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1100 ; 0.001 ; 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): 2782 ; 0.458 ; 4.021 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2781 ; 0.458 ; 4.020 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3474 ; 0.829 ; 6.028 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3475 ; 0.829 ; 6.029 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2862 ; 0.267 ; 4.079 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2859 ; 0.266 ; 4.077 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4184 ; 0.502 ; 6.098 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5629 ; 1.278 ;44.867 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5630 ; 1.278 ;44.872 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 : 2 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 0 A 346 REMARK 3 ORIGIN FOR THE GROUP (A): -13.8830 -71.2050 4.9850 REMARK 3 T TENSOR REMARK 3 T11: 0.1485 T22: 0.1555 REMARK 3 T33: 0.0741 T12: -0.0039 REMARK 3 T13: -0.0326 T23: 0.0032 REMARK 3 L TENSOR REMARK 3 L11: 0.5353 L22: 0.5634 REMARK 3 L33: 0.4455 L12: -0.0840 REMARK 3 L13: -0.0367 L23: -0.1235 REMARK 3 S TENSOR REMARK 3 S11: 0.0107 S12: 0.1157 S13: 0.0921 REMARK 3 S21: -0.1090 S22: -0.0120 S23: -0.0003 REMARK 3 S31: -0.0475 S32: 0.0079 S33: 0.0013 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -59.4100 -58.4560 -5.0830 REMARK 3 T TENSOR REMARK 3 T11: 0.1264 T22: 0.1299 REMARK 3 T33: 0.0626 T12: 0.0063 REMARK 3 T13: 0.0151 T23: 0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.6337 L22: 0.5123 REMARK 3 L33: 0.4829 L12: 0.1850 REMARK 3 L13: 0.2785 L23: 0.0801 REMARK 3 S TENSOR REMARK 3 S11: -0.0163 S12: -0.0946 S13: -0.0394 REMARK 3 S21: 0.0593 S22: 0.0030 S23: -0.0554 REMARK 3 S31: 0.0322 S32: 0.0007 S33: 0.0133 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.10 REMARK 3 ION PROBE RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 7K9P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000252004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 25066 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : MFX REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE MFX REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.277 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : SLAC EPIX10K 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.9.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48524 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 33.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 101.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 70.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.200 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: 6XDH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NENDOU PROTEIN 75 MG/ML (20 MM HEPES REMARK 280 PH 7.5, 150MM NACL, 1MM TCEP) IS ADDED TO THE PRECIPITANT REMARK 280 SOLUTION (100MM NA CITRATE PH 5.5, 20% PEG 1000, 20% 2-METHYL-2, REMARK 280 4-PENTANEDIOL (MPD)) IN A 1:7 PROTEIN:PRECIPITANT RATIO WITH REMARK 280 AGITATION AT 295K OVERNIGHT., BATCH MODE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.50000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.50000 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 58.50000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 89850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -119.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -77.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -133.36791 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 77.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -133.36791 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 -77.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -133.36791 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 58.50000 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 77.00000 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 -133.36791 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 58.50000 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 58.50000 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 GLY A -1 REMARK 465 GLN A 347 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 88.80 26.74 REMARK 500 ASN A 30 22.50 49.76 REMARK 500 ASN A 83 38.45 70.84 REMARK 500 VAL A 102 -50.59 -133.45 REMARK 500 GLU A 171 -44.52 -133.59 REMARK 500 VAL A 237 -60.00 -104.04 REMARK 500 LEU A 249 65.54 69.50 REMARK 500 ASN B 29 -123.47 53.25 REMARK 500 ASN B 83 38.17 70.87 REMARK 500 VAL B 102 -50.62 -133.27 REMARK 500 GLU B 171 -45.75 -133.50 REMARK 500 VAL B 237 -60.32 -104.13 REMARK 500 LEU B 249 64.50 69.66 REMARK 500 ASP B 268 78.99 -102.13 REMARK 500 LEU B 346 86.45 -58.99 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 507 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 508 DISTANCE = 7.36 ANGSTROMS REMARK 525 HOH A 509 DISTANCE = 13.01 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT B 501 DBREF 7K9P A 2 347 UNP P0DTD1 R1AB_SARS2 6453 6798 DBREF 7K9P B 2 347 UNP P0DTD1 R1AB_SARS2 6453 6798 SEQADV 7K9P GLY A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7K9P HIS A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7K9P MET A 1 UNP P0DTD1 EXPRESSION TAG SEQADV 7K9P GLY B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 7K9P HIS B 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7K9P MET B 1 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 349 GLY HIS MET SER LEU GLU ASN VAL ALA PHE ASN VAL VAL SEQRES 2 A 349 ASN LYS GLY HIS PHE ASP GLY GLN GLN GLY GLU VAL PRO SEQRES 3 A 349 VAL SER ILE ILE ASN ASN THR VAL TYR THR LYS VAL ASP SEQRES 4 A 349 GLY VAL ASP VAL GLU LEU PHE GLU ASN LYS THR THR LEU SEQRES 5 A 349 PRO VAL ASN VAL ALA PHE GLU LEU TRP ALA LYS ARG ASN SEQRES 6 A 349 ILE LYS PRO VAL PRO GLU VAL LYS ILE LEU ASN ASN LEU SEQRES 7 A 349 GLY VAL ASP ILE ALA ALA ASN THR VAL ILE TRP ASP TYR SEQRES 8 A 349 LYS ARG ASP ALA PRO ALA HIS ILE SER THR ILE GLY VAL SEQRES 9 A 349 CYS SER MET THR ASP ILE ALA LYS LYS PRO THR GLU THR SEQRES 10 A 349 ILE CYS ALA PRO LEU THR VAL PHE PHE ASP GLY ARG VAL SEQRES 11 A 349 ASP GLY GLN VAL ASP LEU PHE ARG ASN ALA ARG ASN GLY SEQRES 12 A 349 VAL LEU ILE THR GLU GLY SER VAL LYS GLY LEU GLN PRO SEQRES 13 A 349 SER VAL GLY PRO LYS GLN ALA SER LEU ASN GLY VAL THR SEQRES 14 A 349 LEU ILE GLY GLU ALA VAL LYS THR GLN PHE ASN TYR TYR SEQRES 15 A 349 LYS LYS VAL ASP GLY VAL VAL GLN GLN LEU PRO GLU THR SEQRES 16 A 349 TYR PHE THR GLN SER ARG ASN LEU GLN GLU PHE LYS PRO SEQRES 17 A 349 ARG SER GLN MET GLU ILE ASP PHE LEU GLU LEU ALA MET SEQRES 18 A 349 ASP GLU PHE ILE GLU ARG TYR LYS LEU GLU GLY TYR ALA SEQRES 19 A 349 PHE GLU HIS ILE VAL TYR GLY ASP PHE SER HIS SER GLN SEQRES 20 A 349 LEU GLY GLY LEU HIS LEU LEU ILE GLY LEU ALA LYS ARG SEQRES 21 A 349 PHE LYS GLU SER PRO PHE GLU LEU GLU ASP PHE ILE PRO SEQRES 22 A 349 MET ASP SER THR VAL LYS ASN TYR PHE ILE THR ASP ALA SEQRES 23 A 349 GLN THR GLY SER SER LYS CYS VAL CYS SER VAL ILE ASP SEQRES 24 A 349 LEU LEU LEU ASP ASP PHE VAL GLU ILE ILE LYS SER GLN SEQRES 25 A 349 ASP LEU SER VAL VAL SER LYS VAL VAL LYS VAL THR ILE SEQRES 26 A 349 ASP TYR THR GLU ILE SER PHE MET LEU TRP CYS LYS ASP SEQRES 27 A 349 GLY HIS VAL GLU THR PHE TYR PRO LYS LEU GLN SEQRES 1 B 349 GLY HIS MET SER LEU GLU ASN VAL ALA PHE ASN VAL VAL SEQRES 2 B 349 ASN LYS GLY HIS PHE ASP GLY GLN GLN GLY GLU VAL PRO SEQRES 3 B 349 VAL SER ILE ILE ASN ASN THR VAL TYR THR LYS VAL ASP SEQRES 4 B 349 GLY VAL ASP VAL GLU LEU PHE GLU ASN LYS THR THR LEU SEQRES 5 B 349 PRO VAL ASN VAL ALA PHE GLU LEU TRP ALA LYS ARG ASN SEQRES 6 B 349 ILE LYS PRO VAL PRO GLU VAL LYS ILE LEU ASN ASN LEU SEQRES 7 B 349 GLY VAL ASP ILE ALA ALA ASN THR VAL ILE TRP ASP TYR SEQRES 8 B 349 LYS ARG ASP ALA PRO ALA HIS ILE SER THR ILE GLY VAL SEQRES 9 B 349 CYS SER MET THR ASP ILE ALA LYS LYS PRO THR GLU THR SEQRES 10 B 349 ILE CYS ALA PRO LEU THR VAL PHE PHE ASP GLY ARG VAL SEQRES 11 B 349 ASP GLY GLN VAL ASP LEU PHE ARG ASN ALA ARG ASN GLY SEQRES 12 B 349 VAL LEU ILE THR GLU GLY SER VAL LYS GLY LEU GLN PRO SEQRES 13 B 349 SER VAL GLY PRO LYS GLN ALA SER LEU ASN GLY VAL THR SEQRES 14 B 349 LEU ILE GLY GLU ALA VAL LYS THR GLN PHE ASN TYR TYR SEQRES 15 B 349 LYS LYS VAL ASP GLY VAL VAL GLN GLN LEU PRO GLU THR SEQRES 16 B 349 TYR PHE THR GLN SER ARG ASN LEU GLN GLU PHE LYS PRO SEQRES 17 B 349 ARG SER GLN MET GLU ILE ASP PHE LEU GLU LEU ALA MET SEQRES 18 B 349 ASP GLU PHE ILE GLU ARG TYR LYS LEU GLU GLY TYR ALA SEQRES 19 B 349 PHE GLU HIS ILE VAL TYR GLY ASP PHE SER HIS SER GLN SEQRES 20 B 349 LEU GLY GLY LEU HIS LEU LEU ILE GLY LEU ALA LYS ARG SEQRES 21 B 349 PHE LYS GLU SER PRO PHE GLU LEU GLU ASP PHE ILE PRO SEQRES 22 B 349 MET ASP SER THR VAL LYS ASN TYR PHE ILE THR ASP ALA SEQRES 23 B 349 GLN THR GLY SER SER LYS CYS VAL CYS SER VAL ILE ASP SEQRES 24 B 349 LEU LEU LEU ASP ASP PHE VAL GLU ILE ILE LYS SER GLN SEQRES 25 B 349 ASP LEU SER VAL VAL SER LYS VAL VAL LYS VAL THR ILE SEQRES 26 B 349 ASP TYR THR GLU ILE SER PHE MET LEU TRP CYS LYS ASP SEQRES 27 B 349 GLY HIS VAL GLU THR PHE TYR PRO LYS LEU GLN HET CIT A 401 13 HET CIT B 501 13 HETNAM CIT CITRIC ACID FORMUL 3 CIT 2(C6 H8 O7) FORMUL 5 HOH *16(H2 O) HELIX 1 AA1 SER A 2 GLY A 14 1 13 HELIX 2 AA2 PRO A 51 LYS A 61 1 11 HELIX 3 AA3 GLU A 69 LEU A 76 1 8 HELIX 4 AA4 GLU A 114 ALA A 118 5 5 HELIX 5 AA5 GLY A 130 ALA A 138 1 9 HELIX 6 AA6 SER A 208 LEU A 217 1 10 HELIX 7 AA7 ALA A 218 TYR A 226 1 9 HELIX 8 AA8 ALA A 232 VAL A 237 1 6 HELIX 9 AA9 LEU A 251 SER A 262 1 12 HELIX 10 AB1 LEU A 299 SER A 309 1 11 HELIX 11 AB2 SER B 2 GLY B 14 1 13 HELIX 12 AB3 PRO B 51 LYS B 61 1 11 HELIX 13 AB4 GLU B 69 LEU B 76 1 8 HELIX 14 AB5 GLU B 114 ALA B 118 5 5 HELIX 15 AB6 GLY B 130 ALA B 138 1 9 HELIX 16 AB7 SER B 208 LEU B 217 1 10 HELIX 17 AB8 ALA B 218 TYR B 226 1 9 HELIX 18 AB9 ALA B 232 VAL B 237 1 6 HELIX 19 AC1 LEU B 251 SER B 262 1 12 HELIX 20 AC2 LEU B 299 SER B 309 1 11 SHEET 1 AA1 3 VAL A 25 ILE A 28 0 SHEET 2 AA1 3 THR A 31 VAL A 36 -1 O TYR A 33 N SER A 26 SHEET 3 AA1 3 VAL A 39 GLU A 45 -1 O LEU A 43 N VAL A 32 SHEET 1 AA2 5 ILE A 80 ALA A 81 0 SHEET 2 AA2 5 VAL A 122 ASP A 125 1 O PHE A 123 N ILE A 80 SHEET 3 AA2 5 GLY A 141 THR A 145 1 O VAL A 142 N PHE A 124 SHEET 4 AA2 5 ASN A 178 VAL A 183 -1 O ASN A 178 N THR A 145 SHEET 5 AA2 5 SER A 155 VAL A 156 -1 N SER A 155 O TYR A 179 SHEET 1 AA3 5 ILE A 80 ALA A 81 0 SHEET 2 AA3 5 VAL A 122 ASP A 125 1 O PHE A 123 N ILE A 80 SHEET 3 AA3 5 GLY A 141 THR A 145 1 O VAL A 142 N PHE A 124 SHEET 4 AA3 5 ASN A 178 VAL A 183 -1 O ASN A 178 N THR A 145 SHEET 5 AA3 5 VAL A 186 VAL A 187 -1 O VAL A 186 N VAL A 183 SHEET 1 AA4 2 TRP A 87 ASP A 88 0 SHEET 2 AA4 2 ALA A 93 PRO A 94 -1 O ALA A 93 N ASP A 88 SHEET 1 AA5 2 THR A 99 ILE A 100 0 SHEET 2 AA5 2 ASP A 107 ALA A 109 1 O ILE A 108 N THR A 99 SHEET 1 AA6 2 ALA A 161 LEU A 163 0 SHEET 2 AA6 2 VAL A 166 LEU A 168 -1 O VAL A 166 N LEU A 163 SHEET 1 AA7 3 PHE A 264 GLU A 267 0 SHEET 2 AA7 3 LYS A 277 ASP A 283 -1 O PHE A 280 N GLU A 267 SHEET 3 AA7 3 SER A 289 VAL A 295 -1 O VAL A 295 N LYS A 277 SHEET 1 AA8 3 SER A 316 ILE A 323 0 SHEET 2 AA8 3 THR A 326 LYS A 335 -1 O PHE A 330 N VAL A 319 SHEET 3 AA8 3 HIS A 338 PRO A 344 -1 O HIS A 338 N LYS A 335 SHEET 1 AA9 3 VAL B 25 ILE B 28 0 SHEET 2 AA9 3 THR B 31 VAL B 36 -1 O TYR B 33 N SER B 26 SHEET 3 AA9 3 VAL B 39 GLU B 45 -1 O LEU B 43 N VAL B 32 SHEET 1 AB1 5 ILE B 80 ALA B 81 0 SHEET 2 AB1 5 VAL B 122 ASP B 125 1 O PHE B 123 N ILE B 80 SHEET 3 AB1 5 GLY B 141 THR B 145 1 O VAL B 142 N PHE B 124 SHEET 4 AB1 5 ASN B 178 VAL B 183 -1 O ASN B 178 N THR B 145 SHEET 5 AB1 5 SER B 155 VAL B 156 -1 N SER B 155 O TYR B 179 SHEET 1 AB2 5 ILE B 80 ALA B 81 0 SHEET 2 AB2 5 VAL B 122 ASP B 125 1 O PHE B 123 N ILE B 80 SHEET 3 AB2 5 GLY B 141 THR B 145 1 O VAL B 142 N PHE B 124 SHEET 4 AB2 5 ASN B 178 VAL B 183 -1 O ASN B 178 N THR B 145 SHEET 5 AB2 5 VAL B 186 VAL B 187 -1 O VAL B 186 N VAL B 183 SHEET 1 AB3 2 TRP B 87 ASP B 88 0 SHEET 2 AB3 2 ALA B 93 PRO B 94 -1 O ALA B 93 N ASP B 88 SHEET 1 AB4 2 THR B 99 ILE B 100 0 SHEET 2 AB4 2 ASP B 107 ALA B 109 1 O ILE B 108 N THR B 99 SHEET 1 AB5 2 ALA B 161 LEU B 163 0 SHEET 2 AB5 2 VAL B 166 LEU B 168 -1 O VAL B 166 N LEU B 163 SHEET 1 AB6 3 PHE B 264 GLU B 267 0 SHEET 2 AB6 3 LYS B 277 ASP B 283 -1 O PHE B 280 N GLU B 267 SHEET 3 AB6 3 SER B 289 VAL B 295 -1 O VAL B 295 N LYS B 277 SHEET 1 AB7 3 SER B 316 ILE B 323 0 SHEET 2 AB7 3 THR B 326 LYS B 335 -1 O PHE B 330 N VAL B 319 SHEET 3 AB7 3 HIS B 338 PRO B 344 -1 O HIS B 338 N LYS B 335 SITE 1 AC1 9 HIS A 235 GLN A 245 LEU A 246 GLY A 247 SITE 2 AC1 9 GLY A 248 HIS A 250 LYS A 290 THR A 341 SITE 3 AC1 9 TYR A 343 SITE 1 AC2 8 HIS B 235 GLN B 245 GLY B 247 GLY B 248 SITE 2 AC2 8 HIS B 250 LYS B 290 THR B 341 TYR B 343 CRYST1 154.000 154.000 117.000 90.00 90.00 120.00 P 63 12 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 0.006494 0.003749 0.000000 0.00000 SCALE2 0.000000 0.007498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008547 0.00000