HEADER VIRAL PROTEIN 08-MAR-23 8CRM TITLE CRYSTAL STRUCTURE OF N-TERMINAL SARS-COV-2 NSP1 IN COMPLEX WITH TITLE 2 FRAGMENT HIT 11C6 REFINED AGAINST ANOMALOUS DIFFRACTION DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOST TRANSLATION INHIBITOR NSP1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LEADER PROTEIN,NON-STRUCTURAL PROTEIN 1,NSP1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, NON-STRUCTURAL PROTEIN 1, FRAGMENT HIT, ANOMALOUS KEYWDS 2 DIFFRACTION, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.MA,V.MIKHAILIK,N.PINOTSIS,M.W.BOWLER,F.KOZIELSKI REVDAT 1 04-OCT-23 8CRM 0 SPRSDE 04-OCT-23 8CRM 8AZ9 JRNL AUTH S.MA,V.MYKHAYLYK,M.W.BOWLER,N.PINOTSIS,F.KOZIELSKI JRNL TITL HIGH-CONFIDENCE PLACEMENT OF FRAGMENTS INTO ELECTRON DENSITY JRNL TITL 2 USING ANOMALOUS DIFFRACTION-A CASE STUDY USING HITS JRNL TITL 3 TARGETING SARS-COV-2 NON-STRUCTURAL PROTEIN 1. JRNL REF INT J MOL SCI V. 24 2023 JRNL REFN ESSN 1422-0067 JRNL PMID 37446375 JRNL DOI 10.3390/IJMS241311197 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MA,S.DAMFO,J.LOU,N.PINOTSIS,M.W.BOWLER,S.HAIDER, REMARK 1 AUTH 2 F.KOZIELSKI REMARK 1 TITL TWO LIGAND-BINDING SITES ON SARS-COV-2 NON-STRUCTURAL REMARK 1 TITL 2 PROTEIN 1 REVEALED BY FRAGMENT-BASED X-RAY SCREENING. REMARK 1 REF INT J MOL SCI V. 23 2022 REMARK 1 REFN ESSN 1422-0067 REMARK 1 PMID 36293303 REMARK 1 DOI 10.1021/CI200227U REMARK 2 REMARK 2 RESOLUTION. 1.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1-4487 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 958 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 35.6300 - 2.7100 0.99 2838 143 0.1592 0.1854 REMARK 3 2 2.7100 - 2.1500 0.99 2631 143 0.1804 0.1849 REMARK 3 3 2.1500 - 1.8800 1.00 2650 123 0.1812 0.1978 REMARK 3 4 1.8800 - 1.7100 0.99 2558 150 0.1967 0.2485 REMARK 3 5 1.7100 - 1.5900 1.00 2575 134 0.2095 0.2516 REMARK 3 6 1.5900 - 1.4900 1.00 2582 122 0.2072 0.2429 REMARK 3 7 1.4900 - 1.4200 1.00 2522 143 0.2790 0.3042 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 1015 REMARK 3 ANGLE : 1.278 1392 REMARK 3 CHIRALITY : 0.084 162 REMARK 3 PLANARITY : 0.016 184 REMARK 3 DIHEDRAL : 10.041 154 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 8CRM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129095. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-21; 01-FEB-23; 01-FEB-23 REMARK 200 TEMPERATURE (KELVIN) : 100; 45; 45 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : ESRF; DIAMOND; DIAMOND REMARK 200 BEAMLINE : MASSIF-1; I23; I23 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9655; 2.75; 4.5 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M; DECTRIS REMARK 200 PILATUS 12M; DECTRIS PILATUS 12M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19328 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.417 REMARK 200 RESOLUTION RANGE LOW (A) : 35.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH; SINGLE REMARK 200 WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 0.2 M NACL AND REMARK 280 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.60250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.40850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 105.90375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.40850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.30125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.40850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 105.90375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.40850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.40850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.30125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.60250 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: MONOMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 412 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 47 CD CE NZ REMARK 470 LYS A 58 CD CE NZ REMARK 470 HIS A 81 CG ND1 CD2 CE1 NE2 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 TYR A 97 O HOH A 301 1.88 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 THR A 78 -121.65 55.32 REMARK 500 ALA A 79 58.14 74.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 73 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8CRM A 10 126 UNP P0DTD1 R1AB_SARS2 10 126 SEQADV 8CRM MET A 9 UNP P0DTD1 INITIATING METHIONINE SEQRES 1 A 118 MET GLU LYS THR HIS VAL GLN LEU SER LEU PRO VAL LEU SEQRES 2 A 118 GLN VAL ARG ASP VAL LEU VAL ARG GLY PHE GLY ASP SER SEQRES 3 A 118 VAL GLU GLU VAL LEU SER GLU ALA ARG GLN HIS LEU LYS SEQRES 4 A 118 ASP GLY THR CYS GLY LEU VAL GLU VAL GLU LYS GLY VAL SEQRES 5 A 118 LEU PRO GLN LEU GLU GLN PRO TYR VAL PHE ILE LYS ARG SEQRES 6 A 118 SER ASP ALA ARG THR ALA PRO HIS GLY HIS VAL MET VAL SEQRES 7 A 118 GLU LEU VAL ALA GLU LEU GLU GLY ILE GLN TYR GLY ARG SEQRES 8 A 118 SER GLY GLU THR LEU GLY VAL LEU VAL PRO HIS VAL GLY SEQRES 9 A 118 GLU ILE PRO VAL ALA TYR ARG LYS VAL LEU LEU ARG LYS SEQRES 10 A 118 ASN HET OF6 A 201 26 HETNAM OF6 1-[2-(3-CHLOROPHENYL)-1,3-THIAZOL-4-YL]-~{N}-METHYL- HETNAM 2 OF6 METHANAMINE HETSYN OF6 1-(2-(3-CHLOROPHENYL)THIAZOL-4-YL)-N-METHYLMETHANAMINE FORMUL 2 OF6 C11 H11 CL N2 S FORMUL 3 HOH *125(H2 O) HELIX 1 AA1 GLN A 22 VAL A 26 5 5 HELIX 2 AA2 SER A 34 GLY A 49 1 16 HELIX 3 AA3 VAL A 60 LEU A 64 5 5 HELIX 4 AA4 ALA A 79 HIS A 83 5 5 SHEET 1 AA1 8 ILE A 95 TYR A 97 0 SHEET 2 AA1 8 VAL A 84 LEU A 92 -1 N ALA A 90 O TYR A 97 SHEET 3 AA1 8 ALA A 117 ARG A 124 1 O LEU A 122 N VAL A 84 SHEET 4 AA1 8 HIS A 13 VAL A 20 -1 N VAL A 20 O ALA A 117 SHEET 5 AA1 8 CYS A 51 VAL A 54 1 O LEU A 53 N PRO A 19 SHEET 6 AA1 8 THR A 103 PRO A 109 -1 O VAL A 108 N GLY A 52 SHEET 7 AA1 8 TYR A 68 ARG A 73 -1 N VAL A 69 O LEU A 107 SHEET 8 AA1 8 VAL A 84 LEU A 92 -1 O VAL A 89 N PHE A 70 CISPEP 1 GLN A 66 PRO A 67 0 -7.60 CRYST1 36.817 36.817 141.205 90.00 90.00 90.00 P 43 21 2 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 0.027161 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007082 0.00000