HEADER HYDROLASE 25-AUG-08 3EA9 TITLE CRYSTAL STRUCTURE OF SARS-COV MAIN PROTEASE QUADRUPLE MUTANT STIF/A TITLE 2 WITH ONE MOLECULE IN ONE ASYMMETRIC UNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SARS-COV MAIN PROTEASE, 3CL-PRO, 3CLP, NSP5; COMPND 5 EC: 3.4.22.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_COMMON: SARS-COV; SOURCE 4 ORGANISM_TAXID: 227859; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS SARS CORONAVIRUS MAIN PROTEASE MUTANT, 3C-LIKE PROTEASE, EXTRA KEYWDS 2 HELICAL DOMAIN, CYTOPLASM, HYDROLASE, MEMBRANE, METAL-BINDING, KEYWDS 3 PROTEASE, RIBOSOMAL FRAMESHIFTING, RNA-BINDING, THIOL PROTEASE, KEYWDS 4 TRANSMEMBRANE, ZINC, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR J.H.SHI,S.JAYARAMAN,J.X.SONG REVDAT 3 01-NOV-23 3EA9 1 REMARK REVDAT 2 10-NOV-21 3EA9 1 SEQADV REVDAT 1 01-SEP-09 3EA9 0 JRNL AUTH J.H.SHI,S.JAYARAMAN,J.X.SONG JRNL TITL CRYSTAL STRUCTURE OF SARS-COV MPRO QUADRUPLE MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.8 REMARK 3 NUMBER OF REFLECTIONS : 14390 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1447 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 42.9740 - 5.1680 0.98 1540 173 0.1610 0.1990 REMARK 3 2 5.1680 - 4.1030 0.99 1522 169 0.1510 0.2160 REMARK 3 3 4.1030 - 3.5850 0.98 1490 165 0.1940 0.2500 REMARK 3 4 3.5850 - 3.2570 0.97 1488 165 0.2190 0.2770 REMARK 3 5 3.2570 - 3.0240 0.94 1429 160 0.2470 0.3410 REMARK 3 6 3.0240 - 2.8450 0.87 1332 150 0.2540 0.3370 REMARK 3 7 2.8450 - 2.7030 0.83 1253 139 0.2490 0.3080 REMARK 3 8 2.7030 - 2.5850 0.76 1146 124 0.2370 0.3180 REMARK 3 9 2.5850 - 2.4860 0.65 997 116 0.2370 0.2980 REMARK 3 10 2.4860 - 2.4000 0.50 746 86 0.2600 0.3680 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 : 0.36 REMARK 3 B_SOL : 50.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.41500 REMARK 3 B22 (A**2) : -1.44400 REMARK 3 B33 (A**2) : 16.85900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.25500 REMARK 3 B23 (A**2) : 0.00000 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 : 0.010 2361 REMARK 3 ANGLE : 1.398 3211 REMARK 3 CHIRALITY : 0.089 364 REMARK 3 PLANARITY : 0.007 418 REMARK 3 DIHEDRAL : 18.580 830 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 3EA9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000049071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 150 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54105 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SAINT, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17520 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : NULL REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21900 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: PDB ENTRY 2H2Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG 6000, 0.1M MES, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 54.35800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.34700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.35800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.34700 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 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 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 236 CG CD CE NZ 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 ASP A 33 -129.58 53.73 REMARK 500 LEU A 50 87.46 -63.51 REMARK 500 ASN A 51 83.23 56.60 REMARK 500 VAL A 73 98.37 -57.01 REMARK 500 HIS A 80 149.88 -175.58 REMARK 500 ASN A 84 -118.26 44.28 REMARK 500 TYR A 154 -96.92 81.21 REMARK 500 CYS A 160 -9.75 -141.20 REMARK 500 PRO A 184 43.47 -92.21 REMARK 500 THR A 190 -159.31 -123.11 REMARK 500 LEU A 220 173.86 -58.78 REMARK 500 LEU A 282 38.23 39.94 REMARK 500 CYS A 300 22.95 -152.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E91 RELATED DB: PDB REMARK 900 RELATED ID: 3EA7 RELATED DB: PDB REMARK 900 RELATED ID: 3EA8 RELATED DB: PDB REMARK 900 RELATED ID: 3EAJ RELATED DB: PDB DBREF 3EA9 A 1 306 UNP P0C6U8 R1A_CVHSA 3241 3546 SEQADV 3EA9 ALA A 284 UNP P0C6U8 SER 3524 ENGINEERED MUTATION SEQADV 3EA9 ALA A 285 UNP P0C6U8 THR 3525 ENGINEERED MUTATION SEQADV 3EA9 ALA A 286 UNP P0C6U8 ILE 3526 ENGINEERED MUTATION SEQADV 3EA9 ALA A 291 UNP P0C6U8 PHE 3531 ENGINEERED MUTATION SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP THR VAL TYR CYS PRO SEQRES 4 A 306 ARG HIS VAL ILE CYS THR ALA GLU ASP MET LEU ASN PRO SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS SER SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS LEU LEU ARG LEU LYS VAL SEQRES 8 A 306 ASP THR SER ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 306 ARG PRO ASN HIS THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY LYS PHE TYR SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 306 THR ASP THR THR ILE THR LEU ASN VAL LEU ALA TRP LEU SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 306 VAL LEU ASP MET CYS ALA ALA LEU LYS GLU LEU LEU GLN SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY ALA ALA ALA SEQRES 23 A 306 LEU GLU ASP GLU ALA THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN FORMUL 2 HOH *31(H2 O) HELIX 1 1 SER A 10 GLY A 15 1 6 HELIX 2 2 HIS A 41 CYS A 44 5 4 HELIX 3 3 THR A 45 LEU A 50 1 6 HELIX 4 4 ASN A 53 ARG A 60 1 8 HELIX 5 5 ILE A 200 ILE A 213 1 14 HELIX 6 6 THR A 226 TYR A 237 1 12 HELIX 7 7 THR A 243 LEU A 250 1 8 HELIX 8 8 LEU A 250 GLY A 258 1 9 HELIX 9 9 ALA A 260 GLY A 275 1 16 HELIX 10 10 THR A 292 GLN A 299 1 8 SHEET 1 A 7 GLN A 74 LEU A 75 0 SHEET 2 A 7 LEU A 67 GLN A 69 -1 N VAL A 68 O LEU A 75 SHEET 3 A 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 A 7 THR A 25 LEU A 32 -1 O GLY A 29 N VAL A 18 SHEET 5 A 7 THR A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 A 7 LEU A 86 LYS A 90 -1 O LEU A 87 N CYS A 38 SHEET 7 A 7 SER A 81 GLN A 83 -1 N GLN A 83 O LEU A 86 SHEET 1 B 5 TYR A 101 PHE A 103 0 SHEET 2 B 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 B 5 VAL A 148 ASP A 153 -1 N ASP A 153 O CYS A 156 SHEET 4 B 5 THR A 111 TYR A 118 -1 N LEU A 115 O VAL A 148 SHEET 5 B 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 C 3 TYR A 101 PHE A 103 0 SHEET 2 C 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 C 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 CISPEP 1 GLY A 2 PHE A 3 0 -20.65 CRYST1 108.716 80.694 51.906 90.00 105.78 90.00 C 1 2 1 4 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 0.009198 0.000000 0.002600 0.00000 SCALE2 0.000000 0.012392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020020 0.00000