HEADER VIRAL PROTEIN 22-MAR-22 7XC4 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 NSP3 MACRODOMAIN 3 (SARS-UNIQUE TITLE 2 DOMAIN-M) IN COMPLEX WITH OXAPROZIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEASE NSP3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 3,NSP3; COMPND 5 EC: 3.4.19.12,3.4.22.-; COMPND 6 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS G-QUADRUPLEX-BINDING, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.LI,Y.LIU,J.GAO,K.RUAN REVDAT 3 29-NOV-23 7XC4 1 REMARK REVDAT 2 07-DEC-22 7XC4 1 JRNL REVDAT 1 23-NOV-22 7XC4 0 JRNL AUTH J.LI,F.ZHONG,M.LI,Y.LIU,L.WANG,M.LIU,F.LI,J.ZHANG,J.WU, JRNL AUTH 2 Y.SHI,Z.ZHANG,X.TU,K.RUAN,J.GAO JRNL TITL TWO BINDING SITES OF SARS-COV-2 MACRODOMAIN 3 PROBED BY JRNL TITL 2 OXAPROZIN AND MECLOMEN. JRNL REF J.MED.CHEM. V. 65 15227 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36356292 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01168 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 19422 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 1017 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 4.0126 - 3.1872 1.00 2809 156 0.1682 0.2239 REMARK 3 2 3.1872 - 2.7850 1.00 2766 149 0.1956 0.2329 REMARK 3 3 2.7850 - 2.5307 1.00 2759 130 0.2084 0.2569 REMARK 3 4 2.5307 - 2.3495 1.00 2743 139 0.1986 0.2298 REMARK 3 5 2.3495 - 2.2110 1.00 2718 137 0.1898 0.2170 REMARK 3 6 2.2110 - 2.1004 0.99 2678 156 0.1956 0.2415 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.59 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7XC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20439 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 1.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : NULL 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: 2W2G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5 M SODIUM FORMATE, PH 6.8, SOAKING REMARK 280 THE FREE-FORM CRYSTALS IN 5 MM OXAPROZIN BUFFER (50 MM MOLECULE REMARK 280 LIQUOR IN DMSO WAS DILUTED WITH THE RESERVOIR BUFFER), VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 92.17300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.00300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.00300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 46.08650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.00300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.00300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 138.25950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.00300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.00300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 46.08650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.00300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.00300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 138.25950 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 92.17300 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 674 REMARK 465 SER A 675 REMARK 465 SER B 674 REMARK 465 SER B 675 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 VAL A 635 -49.17 69.82 REMARK 500 VAL B 635 -49.77 69.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XC4 A 551 675 UNP P0DTC1 R1A_SARS2 1369 1493 DBREF 7XC4 B 551 675 UNP P0DTC1 R1A_SARS2 1369 1493 SEQADV 7XC4 PHE A 547 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC4 GLN A 548 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC4 HIS A 549 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC4 MET A 550 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC4 PHE B 547 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC4 GLN B 548 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC4 HIS B 549 UNP P0DTC1 EXPRESSION TAG SEQADV 7XC4 MET B 550 UNP P0DTC1 EXPRESSION TAG SEQRES 1 A 129 PHE GLN HIS MET GLY THR VAL SER TRP ASN LEU ARG GLU SEQRES 2 A 129 MET LEU ALA HIS ALA GLU GLU THR ARG LYS LEU MET PRO SEQRES 3 A 129 VAL CYS VAL GLU THR LYS ALA ILE VAL SER THR ILE GLN SEQRES 4 A 129 ARG LYS TYR LYS GLY ILE LYS ILE GLN GLU GLY VAL VAL SEQRES 5 A 129 ASP TYR GLY ALA ARG PHE TYR PHE TYR THR SER LYS THR SEQRES 6 A 129 THR VAL ALA SER LEU ILE ASN THR LEU ASN ASP LEU ASN SEQRES 7 A 129 GLU THR LEU VAL THR MET PRO LEU GLY TYR VAL THR HIS SEQRES 8 A 129 GLY LEU ASN LEU GLU GLU ALA ALA ARG TYR MET ARG SER SEQRES 9 A 129 LEU LYS VAL PRO ALA THR VAL SER VAL SER SER PRO ASP SEQRES 10 A 129 ALA VAL THR ALA TYR ASN GLY TYR LEU THR SER SER SEQRES 1 B 129 PHE GLN HIS MET GLY THR VAL SER TRP ASN LEU ARG GLU SEQRES 2 B 129 MET LEU ALA HIS ALA GLU GLU THR ARG LYS LEU MET PRO SEQRES 3 B 129 VAL CYS VAL GLU THR LYS ALA ILE VAL SER THR ILE GLN SEQRES 4 B 129 ARG LYS TYR LYS GLY ILE LYS ILE GLN GLU GLY VAL VAL SEQRES 5 B 129 ASP TYR GLY ALA ARG PHE TYR PHE TYR THR SER LYS THR SEQRES 6 B 129 THR VAL ALA SER LEU ILE ASN THR LEU ASN ASP LEU ASN SEQRES 7 B 129 GLU THR LEU VAL THR MET PRO LEU GLY TYR VAL THR HIS SEQRES 8 B 129 GLY LEU ASN LEU GLU GLU ALA ALA ARG TYR MET ARG SER SEQRES 9 B 129 LEU LYS VAL PRO ALA THR VAL SER VAL SER SER PRO ASP SEQRES 10 B 129 ALA VAL THR ALA TYR ASN GLY TYR LEU THR SER SER HET BJ6 A 701 22 HET BJ6 B 701 22 HETNAM BJ6 3-(4,5-DIPHENYL-1,3-OXAZOL-2-YL)PROPANOIC ACID FORMUL 3 BJ6 2(C18 H15 N O3) FORMUL 5 HOH *212(H2 O) HELIX 1 AA1 ASN A 556 ARG A 568 1 13 HELIX 2 AA2 THR A 577 TYR A 588 1 12 HELIX 3 AA3 THR A 612 ASN A 624 1 13 HELIX 4 AA4 ASN A 640 ARG A 649 1 10 HELIX 5 AA5 SER A 661 THR A 673 1 13 HELIX 6 AA6 ASN B 556 ARG B 568 1 13 HELIX 7 AA7 THR B 577 TYR B 588 1 12 HELIX 8 AA8 THR B 612 ASN B 624 1 13 HELIX 9 AA9 ASN B 640 ARG B 649 1 10 HELIX 10 AB1 SER B 661 THR B 673 1 13 SHEET 1 AA1 3 MET A 550 VAL A 553 0 SHEET 2 AA1 3 ALA A 655 SER A 658 1 O VAL A 657 N GLY A 551 SHEET 3 AA1 3 LEU A 627 THR A 629 1 N THR A 629 O SER A 658 SHEET 1 AA2 3 LEU A 570 CYS A 574 0 SHEET 2 AA2 3 ARG A 603 TYR A 607 1 O TYR A 605 N VAL A 573 SHEET 3 AA2 3 GLY A 596 ASP A 599 -1 N GLY A 596 O PHE A 606 SHEET 1 AA3 3 MET B 550 VAL B 553 0 SHEET 2 AA3 3 ALA B 655 SER B 658 1 O VAL B 657 N GLY B 551 SHEET 3 AA3 3 LEU B 627 THR B 629 1 N THR B 629 O THR B 656 SHEET 1 AA4 3 MET B 571 CYS B 574 0 SHEET 2 AA4 3 ARG B 603 TYR B 607 1 O ARG B 603 N MET B 571 SHEET 3 AA4 3 GLY B 596 ASP B 599 -1 N VAL B 598 O PHE B 604 CRYST1 60.006 60.006 184.346 90.00 90.00 90.00 P 41 21 2 16 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 0.016665 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016665 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005425 0.00000