HEADER HYDROLASE 23-JUL-21 5SBF TITLE PANDDA ANALYSIS GROUP DEPOSITION OF GROUND-STATE MODEL OF SARS-COV-2 TITLE 2 NENDOU COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDYLATE-SPECIFIC ENDORIBONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NENDOU, 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; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER, NSP15, KEYWDS 2 NENDOU, SARS-COV-2, SARS, COVID, COVID19, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.S.GODOY,A.DOUANGAMATH,A.M.NAKAMURA,A.DIAS,T.KROJER,G.D.NOSKE, AUTHOR 2 V.O.GAWILJUK,R.S.FERNANDES,M.FAIRHEAD,A.POWELL,L.DUNNET,A.AIMON, AUTHOR 3 D.FEARON,J.BRANDAO-NETO,R.SKYNER,F.VON DELFT,G.OLIVA REVDAT 3 21-JUN-23 5SBF 1 JRNL REVDAT 2 10-MAY-23 5SBF 1 JRNL REVDAT 1 09-FEB-22 5SBF 0 JRNL AUTH A.S.GODOY,A.M.NAKAMURA,A.DOUANGAMATH,Y.SONG,G.D.NOSKE, JRNL AUTH 2 V.O.GAWRILJUK,R.S.FERNANDES,H.D.M.PEREIRA,K.I.Z.OLIVEIRA, JRNL AUTH 3 D.FEARON,A.DIAS,T.KROJER,M.FAIRHEAD,A.POWELL,L.DUNNET, JRNL AUTH 4 J.BRANDAO-NETO,R.SKYNER,R.CHALK,D.BAJUSZ,M.BEGE,A.BORBAS, JRNL AUTH 5 G.M.KESERU,F.VON DELFT,G.OLIVA JRNL TITL ALLOSTERIC REGULATION AND CRYSTALLOGRAPHIC FRAGMENT JRNL TITL 2 SCREENING OF SARS-COV-2 NSP15 ENDORIBONUCLEASE. JRNL REF NUCLEIC ACIDS RES. V. 51 5255 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37115000 JRNL DOI 10.1093/NAR/GKAD314 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0266 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 129.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 161483 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 8654 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9624 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.4250 REMARK 3 BIN FREE R VALUE SET COUNT : 558 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5498 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 966 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : -0.74000 REMARK 3 B33 (A**2) : 2.39000 REMARK 3 B12 (A**2) : -0.37000 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): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.080 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.779 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5654 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5380 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7674 ; 1.767 ; 1.637 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12416 ; 1.500 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 698 ; 7.173 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;35.724 ;24.420 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 982 ;13.715 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.607 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 740 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6428 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1250 ; 0.007 ; 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): 2792 ; 2.886 ; 2.983 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2791 ; 2.885 ; 2.980 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3490 ; 3.986 ; 4.456 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 : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5SBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1001404296. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 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) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9127 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1560712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 130.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.45800 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 6X1B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA3 CITRATE PH 5,14% W/V REMARK 280 PEG6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 55.70250 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 55.70250 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 55.70250 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 82940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.0 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 -74.99850 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -129.90121 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 74.99850 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -129.90121 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 74.99850 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -129.90121 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 55.70250 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 55.70250 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 -74.99850 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 -129.90121 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 55.70250 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 -2 REMARK 465 GLY B -2 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 ALA A -1 CB REMARK 470 ALA B -1 CB 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 O HOH B 802 O HOH B 944 1.92 REMARK 500 O HOH B 912 O HOH B 915 1.96 REMARK 500 O HOH B 831 O HOH B 974 1.99 REMARK 500 O HOH B 689 O HOH B 808 1.99 REMARK 500 O HOH A 785 O HOH A 899 2.00 REMARK 500 O HOH A 769 O HOH A 881 2.03 REMARK 500 O HOH B 634 O HOH B 819 2.03 REMARK 500 O HOH A 616 O HOH A 882 2.05 REMARK 500 O HOH A 955 O HOH A 961 2.06 REMARK 500 O HOH A 720 O HOH A 752 2.06 REMARK 500 O HOH A 512 O HOH A 787 2.06 REMARK 500 O HOH B 879 O HOH B 911 2.07 REMARK 500 O HOH B 881 O HOH B 935 2.07 REMARK 500 O HOH B 905 O HOH B 931 2.10 REMARK 500 O HOH A 939 O HOH A 960 2.10 REMARK 500 O HOH B 832 O HOH B 951 2.11 REMARK 500 O HOH A 613 O HOH A 927 2.11 REMARK 500 O HOH A 526 O HOH A 633 2.12 REMARK 500 O HOH B 818 O HOH B 935 2.13 REMARK 500 O HOH B 516 O HOH B 567 2.14 REMARK 500 O HOH A 648 O HOH A 941 2.15 REMARK 500 O HOH B 611 O HOH B 901 2.15 REMARK 500 O HOH B 769 O HOH B 858 2.17 REMARK 500 O HOH B 684 O HOH B 884 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 634 O HOH A 775 2445 1.76 REMARK 500 O HOH A 962 O HOH A 962 2445 1.95 REMARK 500 O HOH A 898 O HOH B 851 5555 2.04 REMARK 500 O HOH B 750 O HOH B 892 2545 2.06 REMARK 500 O HOH A 721 O HOH B 928 5555 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 ASN A 28 C ASN A 28 O 0.170 REMARK 500 SER B 25 CB SER B 25 OG -0.090 REMARK 500 ASN B 28 C ASN B 28 O 0.189 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 90 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG B 90 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG B 90 NE - CZ - NH1 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG B 90 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 14 174.18 179.91 REMARK 500 ASN A 28 75.31 45.10 REMARK 500 ASN A 28 -125.64 59.03 REMARK 500 ASN A 29 29.53 24.19 REMARK 500 LEU A 248 62.15 66.54 REMARK 500 TYR A 324 -0.34 71.92 REMARK 500 SER B 1 137.16 -172.62 REMARK 500 HIS B 14 175.07 179.87 REMARK 500 ASN B 28 78.40 36.31 REMARK 500 ASN B 28 -121.74 61.15 REMARK 500 ASN B 29 28.22 27.51 REMARK 500 LEU B 248 64.26 61.73 REMARK 500 TYR B 324 -0.02 72.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 28 -14.71 REMARK 500 ASN B 28 -15.50 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 978 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH B 988 DISTANCE = 6.58 ANGSTROMS DBREF 5SBF A 1 346 UNP P0DTD1 R1AB_SARS2 6453 6798 DBREF 5SBF B 1 346 UNP P0DTD1 R1AB_SARS2 6453 6798 SEQADV 5SBF GLY A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 5SBF ALA A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 5SBF MET A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 5SBF GLY B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 5SBF ALA B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 5SBF MET B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 349 GLY ALA 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 ALA 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 401 13 HETNAM CIT CITRIC ACID FORMUL 3 CIT 2(C6 H8 O7) FORMUL 5 HOH *966(H2 O) HELIX 1 AA1 SER A 1 GLY A 13 1 13 HELIX 2 AA2 PRO A 50 LYS A 60 1 11 HELIX 3 AA3 GLU A 68 LEU A 75 1 8 HELIX 4 AA4 GLU A 113 ALA A 117 5 5 HELIX 5 AA5 GLY A 129 ALA A 137 1 9 HELIX 6 AA6 SER A 207 LEU A 216 1 10 HELIX 7 AA7 ALA A 217 TYR A 225 1 9 HELIX 8 AA8 ALA A 231 VAL A 236 1 6 HELIX 9 AA9 LEU A 250 SER A 261 1 12 HELIX 10 AB1 LEU A 298 SER A 308 1 11 HELIX 11 AB2 SER B 1 GLY B 13 1 13 HELIX 12 AB3 PRO B 50 LYS B 60 1 11 HELIX 13 AB4 GLU B 68 LEU B 75 1 8 HELIX 14 AB5 GLU B 113 ALA B 117 5 5 HELIX 15 AB6 GLY B 129 ALA B 137 1 9 HELIX 16 AB7 SER B 207 LEU B 216 1 10 HELIX 17 AB8 ALA B 217 TYR B 225 1 9 HELIX 18 AB9 ALA B 231 VAL B 236 1 6 HELIX 19 AC1 LEU B 250 SER B 261 1 12 HELIX 20 AC2 LEU B 298 LYS B 307 1 10 SHEET 1 AA1 3 VAL A 24 ILE A 27 0 SHEET 2 AA1 3 THR A 30 VAL A 35 -1 O TYR A 32 N SER A 25 SHEET 3 AA1 3 VAL A 38 GLU A 44 -1 O VAL A 38 N VAL A 35 SHEET 1 AA2 5 ILE A 79 ALA A 80 0 SHEET 2 AA2 5 VAL A 121 ASP A 124 1 O PHE A 122 N ILE A 79 SHEET 3 AA2 5 GLY A 140 THR A 144 1 O VAL A 141 N PHE A 123 SHEET 4 AA2 5 ASN A 177 VAL A 182 -1 O TYR A 179 N LEU A 142 SHEET 5 AA2 5 SER A 154 VAL A 155 -1 N SER A 154 O TYR A 178 SHEET 1 AA3 5 ILE A 79 ALA A 80 0 SHEET 2 AA3 5 VAL A 121 ASP A 124 1 O PHE A 122 N ILE A 79 SHEET 3 AA3 5 GLY A 140 THR A 144 1 O VAL A 141 N PHE A 123 SHEET 4 AA3 5 ASN A 177 VAL A 182 -1 O TYR A 179 N LEU A 142 SHEET 5 AA3 5 VAL A 185 GLN A 187 -1 O GLN A 187 N LYS A 180 SHEET 1 AA4 2 TRP A 86 ASP A 87 0 SHEET 2 AA4 2 ALA A 92 PRO A 93 -1 O ALA A 92 N ASP A 87 SHEET 1 AA5 2 THR A 98 ILE A 99 0 SHEET 2 AA5 2 ASP A 106 ALA A 108 1 O ILE A 107 N THR A 98 SHEET 1 AA6 2 ALA A 160 LEU A 162 0 SHEET 2 AA6 2 VAL A 165 LEU A 167 -1 O LEU A 167 N ALA A 160 SHEET 1 AA7 3 PHE A 263 GLU A 266 0 SHEET 2 AA7 3 LYS A 276 ASP A 282 -1 O THR A 281 N GLU A 264 SHEET 3 AA7 3 SER A 288 VAL A 294 -1 O VAL A 294 N LYS A 276 SHEET 1 AA8 3 SER A 315 ILE A 322 0 SHEET 2 AA8 3 THR A 325 LYS A 334 -1 O PHE A 329 N VAL A 318 SHEET 3 AA8 3 HIS A 337 PRO A 343 -1 O THR A 340 N TRP A 332 SHEET 1 AA9 3 VAL B 24 ILE B 27 0 SHEET 2 AA9 3 THR B 30 VAL B 35 -1 O TYR B 32 N SER B 25 SHEET 3 AA9 3 VAL B 38 GLU B 44 -1 O LEU B 42 N VAL B 31 SHEET 1 AB1 5 ILE B 79 ALA B 80 0 SHEET 2 AB1 5 VAL B 121 ASP B 124 1 O PHE B 122 N ILE B 79 SHEET 3 AB1 5 GLY B 140 THR B 144 1 O VAL B 141 N PHE B 123 SHEET 4 AB1 5 ASN B 177 VAL B 182 -1 O ASN B 177 N THR B 144 SHEET 5 AB1 5 SER B 154 VAL B 155 -1 N SER B 154 O TYR B 178 SHEET 1 AB2 5 ILE B 79 ALA B 80 0 SHEET 2 AB2 5 VAL B 121 ASP B 124 1 O PHE B 122 N ILE B 79 SHEET 3 AB2 5 GLY B 140 THR B 144 1 O VAL B 141 N PHE B 123 SHEET 4 AB2 5 ASN B 177 VAL B 182 -1 O ASN B 177 N THR B 144 SHEET 5 AB2 5 VAL B 185 VAL B 186 -1 O VAL B 185 N VAL B 182 SHEET 1 AB3 2 TRP B 86 ASP B 87 0 SHEET 2 AB3 2 ALA B 92 PRO B 93 -1 O ALA B 92 N ASP B 87 SHEET 1 AB4 2 THR B 98 ILE B 99 0 SHEET 2 AB4 2 ASP B 106 ALA B 108 1 O ILE B 107 N THR B 98 SHEET 1 AB5 2 ALA B 160 LEU B 162 0 SHEET 2 AB5 2 VAL B 165 LEU B 167 -1 O VAL B 165 N LEU B 162 SHEET 1 AB6 3 PHE B 263 GLU B 266 0 SHEET 2 AB6 3 LYS B 276 ASP B 282 -1 O PHE B 279 N GLU B 266 SHEET 3 AB6 3 SER B 288 VAL B 294 -1 O VAL B 294 N LYS B 276 SHEET 1 AB7 3 SER B 315 ILE B 322 0 SHEET 2 AB7 3 THR B 325 LYS B 334 -1 O PHE B 329 N VAL B 318 SHEET 3 AB7 3 HIS B 337 PRO B 343 -1 O GLU B 339 N TRP B 332 CRYST1 149.997 149.997 111.405 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 0.006667 0.003849 0.000000 0.00000 SCALE2 0.000000 0.007698 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008976 0.00000