HEADER HYDROLASE 10-MAR-10 3M3T TITLE SARS-COV MAIN PROTEASE MONOMERIC ARG298ALA MUTANT WITH N-TERMINAL TITLE 2 ADDITIONAL RESIDUES (GLY-SER) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3CL-PRO, 3CLP; 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; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS SARS PROTEASE ARG298ALA MONOMERIC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.SHI,J.X.SONG REVDAT 2 01-NOV-23 3M3T 1 SEQADV REVDAT 1 23-MAR-11 3M3T 0 JRNL AUTH J.H.SHI,J.X.SONG JRNL TITL SARS-COV MAIN PROTEASE WITH N-TERMINAL EXTENSION REGULATED JRNL TITL 2 BY MUTATION ON C-TERMINAL DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.4 REMARK 3 NUMBER OF REFLECTIONS : 5360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 581 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2365 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.89100 REMARK 3 B22 (A**2) : -7.88900 REMARK 3 B33 (A**2) : 1.99700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.57400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 34.19 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3M3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0810 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6356 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 95.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.28500 REMARK 200 R SYM FOR SHELL (I) : 0.22800 REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB CODE 2H2Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% 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: 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 33.10500 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 GLN A 306 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 MET A 6 150.06 -43.83 REMARK 500 ASP A 33 -116.66 55.24 REMARK 500 ALA A 46 -35.42 -34.58 REMARK 500 ASP A 48 45.47 -68.56 REMARK 500 ASN A 51 78.26 -164.88 REMARK 500 ILE A 59 1.99 -65.40 REMARK 500 SER A 62 -158.78 -114.84 REMARK 500 ASN A 84 -108.81 65.80 REMARK 500 ASP A 92 24.26 -78.96 REMARK 500 LYS A 97 44.15 -90.81 REMARK 500 ILE A 106 -164.16 -60.19 REMARK 500 ASN A 119 -19.82 68.36 REMARK 500 SER A 144 -150.48 -97.89 REMARK 500 CYS A 145 136.70 137.65 REMARK 500 TYR A 154 -102.53 72.79 REMARK 500 HIS A 164 -77.11 -112.58 REMARK 500 PRO A 184 21.02 -77.77 REMARK 500 GLN A 192 -3.52 -147.87 REMARK 500 ALA A 193 30.36 -79.99 REMARK 500 ARG A 217 -30.82 -130.14 REMARK 500 TRP A 218 -35.96 -36.43 REMARK 500 ASN A 274 -18.34 -145.70 REMARK 500 ASN A 277 62.79 69.05 REMARK 500 ASP A 289 19.37 -146.43 REMARK 500 SER A 301 -85.53 -40.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QCY RELATED DB: PDB REMARK 900 SAME MUTANT BUT NO ADDITIONAL RESIDUE REMARK 900 RELATED ID: 3M3S RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SARS-COV MAIN PROTEASE ASN214ALA MUTANT WITH REMARK 900 AUTHORIZE N-TERMINUS REMARK 900 RELATED ID: 3M3V RELATED DB: PDB REMARK 900 SARS-COV MAIN PROTEASE TRIPLE MUTANT STI/A WITH TWO N-TERMINAL REMARK 900 ADDITIONAL RESIDUE (GLY-SER) DBREF 3M3T A 1 306 UNP P0C6U8 R1A_CVHSA 3241 3546 SEQADV 3M3T GLY A -1 UNP P0C6U8 EXPRESSION TAG SEQADV 3M3T SER A 0 UNP P0C6U8 EXPRESSION TAG SEQADV 3M3T ALA A 298 UNP P0C6U8 ARG 3538 ENGINEERED MUTATION SEQRES 1 A 308 GLY SER SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY SEQRES 2 A 308 LYS VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR SEQRES 3 A 308 THR THR LEU ASN GLY LEU TRP LEU ASP ASP THR VAL TYR SEQRES 4 A 308 CYS PRO ARG HIS VAL ILE CYS THR ALA GLU ASP MET LEU SEQRES 5 A 308 ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN SEQRES 6 A 308 HIS SER PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG SEQRES 7 A 308 VAL ILE GLY HIS SER MET GLN ASN CYS LEU LEU ARG LEU SEQRES 8 A 308 LYS VAL ASP THR SER ASN PRO LYS THR PRO LYS TYR LYS SEQRES 9 A 308 PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU SEQRES 10 A 308 ALA CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS SEQRES 11 A 308 ALA MET ARG PRO ASN HIS THR ILE LYS GLY SER PHE LEU SEQRES 12 A 308 ASN GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR SEQRES 13 A 308 ASP CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU SEQRES 14 A 308 PRO THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY LYS SEQRES 15 A 308 PHE TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA SEQRES 16 A 308 ALA GLY THR ASP THR THR ILE THR LEU ASN VAL LEU ALA SEQRES 17 A 308 TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE SEQRES 18 A 308 LEU ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU SEQRES 19 A 308 VAL ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP SEQRES 20 A 308 HIS VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY SEQRES 21 A 308 ILE ALA VAL LEU ASP MET CYS ALA ALA LEU LYS GLU LEU SEQRES 22 A 308 LEU GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER SEQRES 23 A 308 THR ILE LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL SEQRES 24 A 308 ALA GLN CYS SER GLY VAL THR PHE GLN FORMUL 2 HOH *13(H2 O) HELIX 1 1 VAL A 13 GLY A 15 5 3 HELIX 2 2 HIS A 41 CYS A 44 5 4 HELIX 3 3 ASN A 53 ILE A 59 1 7 HELIX 4 4 GLY A 138 ASN A 142 5 5 HELIX 5 5 ILE A 200 ASN A 214 1 15 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 ASN A 274 1 15 HELIX 10 10 THR A 292 CYS A 300 1 9 SHEET 1 A 7 VAL A 73 LEU A 75 0 SHEET 2 A 7 PHE A 66 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 A 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69 SHEET 4 A 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 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 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 A 7 VAL A 77 GLN A 83 -1 N ILE A 78 O LYS A 90 SHEET 1 B 5 LYS A 100 PHE A 103 0 SHEET 2 B 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 B 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 B 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 B 5 SER A 121 ALA A 129 -1 O TYR A 126 N VAL A 114 SHEET 1 C 3 LYS A 100 PHE A 103 0 SHEET 2 C 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 C 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162 CRYST1 33.129 66.210 64.496 90.00 109.15 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 0.030185 0.000000 0.010482 0.00000 SCALE2 0.000000 0.015103 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016413 0.00000