HEADER PROTEIN BINDING 12-DEC-23 8RF4 TITLE CRYSTAL STRUCTURE OF N-TERMINAL SARS-COV-2 NSP1 IN COMPLEX WITH TITLE 2 FRAGMENT HIT 9D4 REFINED AGAINST THE 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 VIRAL PROTEIN, SARS-COV-2, NON-STRUCTURAL PROTEIN 1, NSP1, FRAGMENT KEYWDS 2 HIT, ANOMALOUS DIFFRACTION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.MA,S.DAMFO,V.MYKHAYLYK,F.KOZIELSKI REVDAT 1 19-JUN-24 8RF4 0 JRNL AUTH S.MA,S.DAMFO,M.W.BOWLER,V.MYKHAYLYK,F.KOZIELSKI JRNL TITL HIGH-CONFIDENCE PLACEMENT OF LOW-OCCUPANCY FRAGMENTS INTO JRNL TITL 2 ELECTRON DENSITY USING THE ANOMALOUS SIGNAL OF SULFUR AND JRNL TITL 3 HALOGEN ATOMS. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 80 451 2024 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 38841886 JRNL DOI 10.1107/S2059798324004480 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.MA,V.MYKHAYLYK,M.W.BOWLER,N.PINOTSIS,F.KOZIELSKI REMARK 1 TITL HIGH-CONFIDENCE PLACEMENT OF FRAGMENTS INTO ELECTRON DENSITY REMARK 1 TITL 2 USING ANOMALOUS DIFFRACTION-A CASE STUDY USING HITS REMARK 1 TITL 3 TARGETING SARS-COV-2 NON-STRUCTURAL PROTEIN 1. REMARK 1 REF INT J MOL SCI V. 24 2023 REMARK 1 REFN ESSN 1422-0067 REMARK 1 PMID 37446375 REMARK 2 REMARK 2 RESOLUTION. 1.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1-4487-000) 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) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 37808 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1885 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 35.7600 - 2.6000 0.96 3091 175 0.1778 0.2038 REMARK 3 2 2.6000 - 2.0700 0.99 2991 146 0.1885 0.2033 REMARK 3 3 2.0700 - 1.8100 0.98 2926 154 0.1705 0.1903 REMARK 3 4 1.8100 - 1.6400 0.97 2866 148 0.1597 0.1994 REMARK 3 5 1.6400 - 1.5200 0.96 2850 135 0.1643 0.1970 REMARK 3 6 1.5200 - 1.4300 0.96 2808 139 0.1741 0.2383 REMARK 3 7 1.4300 - 1.3600 0.95 2764 141 0.1963 0.2456 REMARK 3 8 1.3600 - 1.3000 0.95 2735 165 0.2129 0.2436 REMARK 3 9 1.3000 - 1.2500 0.93 2673 147 0.2976 0.3283 REMARK 3 10 1.2500 - 1.2100 0.94 2724 132 0.2588 0.2805 REMARK 3 11 1.2100 - 1.1700 0.93 2694 136 0.2618 0.2910 REMARK 3 12 1.1700 - 1.1400 0.93 2661 155 0.2849 0.2856 REMARK 3 13 1.1400 - 1.1100 0.74 2140 112 0.4251 0.4034 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.980 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 : 0.009 969 REMARK 3 ANGLE : 1.240 1318 REMARK 3 CHIRALITY : 0.100 150 REMARK 3 PLANARITY : 0.010 172 REMARK 3 DIHEDRAL : 8.731 135 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 8RF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292135294. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-23; 28-JUL-23 REMARK 200 TEMPERATURE (KELVIN) : 100; 80 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; DIAMOND REMARK 200 BEAMLINE : MASSIF-1; I23 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96546; 2.75520 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M; DECTRIS REMARK 200 PILATUS 12M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN 10, 2022 BUILT=20220820 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38471 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.107 REMARK 200 RESOLUTION RANGE LOW (A) : 35.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 24.00 REMARK 200 R MERGE (I) : 0.15300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 19.60 REMARK 200 R MERGE FOR SHELL (I) : 6.08200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE 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 (%): 33.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTALLISATION CONDITION USED IS REMARK 280 INDEX 71 (CAT. NO.: HR2-944-71; HAMPTON RESEARCH, ALISO VIEJO, REMARK 280 CA, USA) CONTAINING 0.1 M BIS-TRIS PH 6.5, 0.2 M NACL AND 25% W/ REMARK 280 V POLYETHYLENE GLYCOL 3350., 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 70.76900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.47900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.47900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.15350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.47900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.47900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.38450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.47900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.47900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 106.15350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.47900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.47900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.38450 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 70.76900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 377 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 GLU A 10 CG CD OE1 OE2 REMARK 470 LYS A 47 CD CE NZ REMARK 470 LYS A 58 CD CE NZ REMARK 470 ASP A 75 OD1 REMARK 470 THR A 78 CB OG1 CG2 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 LEU A 53 C LEU A 53 O 0.122 REMARK 500 MET A 85 C MET A 85 O 0.126 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 0.19 SIDE CHAIN REMARK 500 ARG A 77 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8RF4 A 10 126 UNP P0DTD1 R1AB_SARS2 10 126 SEQADV 8RF4 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 EQT A 201 22 HETNAM EQT 4-CHLORANYL-1~{H}-INDAZOL-3-AMINE FORMUL 2 EQT C7 H6 CL N3 FORMUL 3 HOH *77(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 -8.42 CRYST1 36.958 36.958 141.538 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 0.027058 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007065 0.00000