HEADER HYDROLASE 30-MAR-20 6WCF TITLE CRYSTAL STRUCTURE OF ADP RIBOSE PHOSPHATASE OF NSP3 FROM SARS-COV-2 IN TITLE 2 COMPLEX WITH MES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NSP3,ADP RIBOSE PHOSPHATASE,PL2-PRO,PAPAIN-LIKE PROTEASE, COMPND 5 PAPAIN-LIKE PROTEINASE,PL-PRO; COMPND 6 EC: 3.4.19.121, 3.4.22.-; COMPND 7 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_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS SARS CORONAVIRUS, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS KEYWDS 2 OF INFECTIOUS DISEASES, CSGID, VIRAL PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.MICHALSKA,Y.KIM,R.JEDRZEJCZAK,N.MALTSEVA,M.ENDRES,A.MESECAR, AUTHOR 2 A.JOACHIMIAK,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID) REVDAT 8 18-OCT-23 6WCF 1 REMARK REVDAT 7 18-AUG-21 6WCF 1 AUTHOR REVDAT 6 27-JAN-21 6WCF 1 COMPND REVDAT 5 14-OCT-20 6WCF 1 COMPND SOURCE REVDAT 4 30-SEP-20 6WCF 1 JRNL REVDAT 3 06-MAY-20 6WCF 1 COMPND SOURCE DBREF SEQADV REVDAT 2 22-APR-20 6WCF 1 SOURCE REVDAT 1 15-APR-20 6WCF 0 JRNL AUTH K.MICHALSKA,Y.KIM,R.JEDRZEJCZAK,N.I.MALTSEVA,L.STOLS, JRNL AUTH 2 M.ENDRES,A.JOACHIMIAK JRNL TITL CRYSTAL STRUCTURES OF SARS-COV-2 ADP-RIBOSE PHOSPHATASE: JRNL TITL 2 FROM THE APO FORM TO LIGAND COMPLEXES. JRNL REF IUCRJ V. 7 814 2020 JRNL REFN ESSN 2052-2525 JRNL PMID 32939273 JRNL DOI 10.1107/S2052252520009653 REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3409 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) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 64228 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 3250 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 33.1300 - 3.0300 0.98 2776 142 0.1295 0.1608 REMARK 3 2 3.0300 - 2.4000 1.00 2795 133 0.1309 0.1528 REMARK 3 3 2.4000 - 2.1000 0.96 2651 141 0.1178 0.1448 REMARK 3 4 2.1000 - 1.9100 0.99 2696 160 0.1202 0.1465 REMARK 3 5 1.9100 - 1.7700 1.00 2705 131 0.1191 0.1370 REMARK 3 6 1.7700 - 1.6700 0.99 2725 153 0.1124 0.1448 REMARK 3 7 1.6700 - 1.5800 0.95 2593 146 0.1043 0.1432 REMARK 3 8 1.5800 - 1.5100 0.99 2675 119 0.0964 0.1106 REMARK 3 9 1.5100 - 1.4600 0.99 2746 128 0.0996 0.1256 REMARK 3 10 1.4600 - 1.4100 1.00 2731 134 0.1073 0.1446 REMARK 3 11 1.4100 - 1.3600 1.00 2731 129 0.1068 0.1451 REMARK 3 12 1.3600 - 1.3200 0.94 2539 126 0.1115 0.1445 REMARK 3 13 1.3200 - 1.2900 0.96 2637 154 0.1133 0.1552 REMARK 3 14 1.2900 - 1.2600 0.99 2648 148 0.1182 0.1438 REMARK 3 15 1.2600 - 1.2300 0.99 2671 161 0.1253 0.1884 REMARK 3 16 1.2300 - 1.2000 1.00 2711 140 0.1321 0.1539 REMARK 3 17 1.2000 - 1.1800 0.99 2702 137 0.1426 0.1544 REMARK 3 18 1.1800 - 1.1600 0.94 2560 116 0.1600 0.1603 REMARK 3 19 1.1600 - 1.1300 0.97 2599 165 0.1635 0.1889 REMARK 3 20 1.1300 - 1.1200 0.98 2685 155 0.1800 0.1923 REMARK 3 21 1.1200 - 1.1000 0.98 2579 157 0.1940 0.2435 REMARK 3 22 1.1000 - 1.0800 0.99 2679 162 0.2126 0.2274 REMARK 3 23 1.0800 - 1.0650 0.79 2144 113 0.2497 0.2600 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.078 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.415 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.35 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 1470 REMARK 3 ANGLE : 1.407 2009 REMARK 3 CHIRALITY : 0.091 230 REMARK 3 PLANARITY : 0.008 261 REMARK 3 DIHEDRAL : 20.503 552 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 6WCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000248016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64283 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.065 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 1.11000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6W6Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.5, 30% W/V PEG4000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 16.58900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 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 GLU A 2 REMARK 465 VAL A 3 REMARK 465 GLU A 170 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 LYS A 31 64.25 38.36 REMARK 500 HIS A 86 -127.93 52.01 REMARK 500 THR A 149 -143.94 -67.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6W6Y RELATED DB: PDB REMARK 900 RELATED ID: 6W02 RELATED DB: PDB REMARK 900 RELATED ID: 6VXS RELATED DB: PDB DBREF 6WCF A 2 170 UNP P0DTD1 R1AB_SARS2 1024 1192 SEQADV 6WCF GLY A 1 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 170 GLY GLU VAL ASN SER PHE SER GLY TYR LEU LYS LEU THR SEQRES 2 A 170 ASP ASN VAL TYR ILE LYS ASN ALA ASP ILE VAL GLU GLU SEQRES 3 A 170 ALA LYS LYS VAL LYS PRO THR VAL VAL VAL ASN ALA ALA SEQRES 4 A 170 ASN VAL TYR LEU LYS HIS GLY GLY GLY VAL ALA GLY ALA SEQRES 5 A 170 LEU ASN LYS ALA THR ASN ASN ALA MET GLN VAL GLU SER SEQRES 6 A 170 ASP ASP TYR ILE ALA THR ASN GLY PRO LEU LYS VAL GLY SEQRES 7 A 170 GLY SER CYS VAL LEU SER GLY HIS ASN LEU ALA LYS HIS SEQRES 8 A 170 CYS LEU HIS VAL VAL GLY PRO ASN VAL ASN LYS GLY GLU SEQRES 9 A 170 ASP ILE GLN LEU LEU LYS SER ALA TYR GLU ASN PHE ASN SEQRES 10 A 170 GLN HIS GLU VAL LEU LEU ALA PRO LEU LEU SER ALA GLY SEQRES 11 A 170 ILE PHE GLY ALA ASP PRO ILE HIS SER LEU ARG VAL CYS SEQRES 12 A 170 VAL ASP THR VAL ARG THR ASN VAL TYR LEU ALA VAL PHE SEQRES 13 A 170 ASP LYS ASN LEU TYR ASP LYS LEU VAL SER SER PHE LEU SEQRES 14 A 170 GLU HET MES A 201 25 HET MES A 202 25 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 MES 2(C6 H13 N O4 S) FORMUL 4 HOH *196(H2 O) HELIX 1 AA1 ASP A 22 LYS A 31 1 10 HELIX 2 AA2 GLY A 47 THR A 57 1 11 HELIX 3 AA3 ASN A 59 GLY A 73 1 15 HELIX 4 AA4 ASN A 99 GLY A 103 5 5 HELIX 5 AA5 GLN A 107 ASN A 115 1 9 HELIX 6 AA6 PHE A 116 HIS A 119 5 4 HELIX 7 AA7 ASP A 135 VAL A 147 1 13 HELIX 8 AA8 ASP A 157 LEU A 169 1 13 SHEET 1 AA1 4 LEU A 10 LYS A 11 0 SHEET 2 AA1 4 VAL A 16 LYS A 19 -1 O ILE A 18 N LEU A 10 SHEET 3 AA1 4 ASN A 150 ALA A 154 1 O LEU A 153 N TYR A 17 SHEET 4 AA1 4 VAL A 121 ALA A 124 1 N LEU A 122 O TYR A 152 SHEET 1 AA2 3 VAL A 34 ALA A 38 0 SHEET 2 AA2 3 HIS A 91 VAL A 95 1 O VAL A 95 N ASN A 37 SHEET 3 AA2 3 SER A 80 SER A 84 -1 N LEU A 83 O CYS A 92 SITE 1 AC1 12 ALA A 38 ASN A 40 LYS A 44 SER A 128 SITE 2 AC1 12 ALA A 129 GLY A 130 ILE A 131 PHE A 132 SITE 3 AC1 12 HOH A 311 HOH A 350 HOH A 400 HOH A 428 SITE 1 AC2 10 GLY A 46 GLY A 47 GLY A 51 ALA A 52 SITE 2 AC2 10 LYS A 55 THR A 71 ASN A 72 HOH A 303 SITE 3 AC2 10 HOH A 333 HOH A 423 CRYST1 37.169 33.178 60.620 90.00 96.11 90.00 P 1 21 1 2 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 0.026904 0.000000 0.002881 0.00000 SCALE2 0.000000 0.030140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016591 0.00000