10 20 30 40 50 60 70 80 4X2X - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 27-NOV-14 4X2X
TITLE CRYSTAL STRUCTURE OF THE MURINE NOROVIRUS NS6 PROTEASE (INACTIVE C139A TITLE 2 MUTANT) WITH A C-TERMINAL EXTENSION TO INCLUDE RESIDUES P1 PRIME - P4 TITLE 3 PRIME OF NS7
COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS6 PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 998-1173; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MURINE NOROVIRUS 1; SOURCE 3 ORGANISM_TAXID: 223997; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VARIANT: PLYSS
KEYWDS MURINE NOROVIRUS PROTEASE, VIRAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR E.N.LEEN,H.CROMWELL JR,H.FERNANDES,S.CURRY
REVDAT 3 18-MAR-15 4X2X 1 JRNL REVDAT 2 25-FEB-15 4X2X 1 JRNL REVDAT 1 18-FEB-15 4X2X 0
JRNL AUTH H.FERNANDES,E.N.LEEN,H.CROMWELL,M.P.PFEIL,S.CURRY JRNL TITL STRUCTURE DETERMINATION OF MURINE NOROVIRUS NS6 PROTEASES JRNL TITL 2 WITH C-TERMINAL EXTENSIONS DESIGNED TO PROBE JRNL TITL 3 PROTEASE-SUBSTRATE INTERACTIONS. JRNL REF PEERJ V. 3 E798 2015 JRNL REFN ESSN 2167-8359 JRNL PMID 25755927 JRNL DOI 10.7717/PEERJ.798
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.N.LEEN,G.BAEZA,S.CURRY REMARK 1 TITL STRUCTURE OF A MURINE NOROVIRUS NS6 PROTEASE-PRODUCT COMPLEX REMARK 1 TITL 2 REVEALED BY ADVENTITIOUS CRYSTALLISATION. REMARK 1 REF PLOS ONE V. 7 38723 2012 REMARK 1 REFN ESSN 1932-6203 REMARK 1 PMID 22685603 REMARK 1 DOI 10.1371/JOURNAL.PONE.0038723
REMARK 2 REMARK 2 RESOLUTION. 2.47 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.11 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 5705 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 286 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 38.1121 - 3.1147 1.00 2767 147 0.1926 0.2238 REMARK 3 2 3.1147 - 2.4723 0.98 2652 139 0.2429 0.3166 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.82 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 1251 REMARK 3 ANGLE : 1.083 1700 REMARK 3 CHIRALITY : 0.070 195 REMARK 3 PLANARITY : 0.005 213 REMARK 3 DIHEDRAL : 13.774 425 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 4X2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-14. REMARK 100 THE DEPOSITION ID IS D_1000204975.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 - 7.5 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5711 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.472 REMARK 200 RESOLUTION RANGE LOW (A) : 38.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 38.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.10600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.940 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: 4ASH REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KSCN, 0.1 M BIS-TRIS PROPANE PH REMARK 280 6.5-7.5, 20% W/V PEG 3350, CRYO 30% (V/V) PEG 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K
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 44.09500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.09500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.68000 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: 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: 8630 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 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 125 REMARK 465 ASN A 126 REMARK 465 ALA A 127 REMARK 465 LYS A 128 REMARK 465 ALA A 129 REMARK 465 GLN A 130 REMARK 465 ASP A 131 REMARK 465 LEU A 132 REMARK 465 ARG A 162 REMARK 465 SER A 163
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 29 O HOH A 201 2.12 REMARK 500 N GLY A 137 O HOH A 222 2.13 REMARK 500 O HOH A 218 O HOH A 219 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ASN A 165 -23.59 79.09 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ASH RELATED DB: PDB REMARK 900 THIS ENTRY CONTAINS C TERMINAL EXTENSION TO INCLUDE RESIDUE P1 REMARK 900 PRIME TO P4 PRIME OF NS7 IN ADDITION TO 4ASH REMARK 900 RELATED ID: 4X2V RELATED DB: PDB REMARK 900 RELATED ID: 4X2W RELATED DB: PDB
DBREF 4X2X A 4 179 UNP Q80J95 Q80J95_9CALI 998 1173
SEQADV 4X2X ALA A 139 UNP Q80J95 CYS 1133 ENGINEERED MUTATION
SEQRES 1 A 176 SER ILE TRP SER ARG VAL VAL GLN PHE GLY THR GLY TRP SEQRES 2 A 176 GLY PHE TRP VAL SER GLY HIS VAL PHE ILE THR ALA LYS SEQRES 3 A 176 HIS VAL ALA PRO PRO LYS GLY THR GLU ILE PHE GLY ARG SEQRES 4 A 176 LYS PRO GLY ASP PHE THR VAL THR SER SER GLY ASP PHE SEQRES 5 A 176 LEU LYS TYR TYR PHE THR SER ALA VAL ARG PRO ASP ILE SEQRES 6 A 176 PRO ALA MET VAL LEU GLU ASN GLY CYS GLN GLU GLY VAL SEQRES 7 A 176 VAL ALA SER VAL LEU VAL LYS ARG ALA SER GLY GLU MET SEQRES 8 A 176 LEU ALA LEU ALA VAL ARG MET GLY SER GLN ALA ALA ILE SEQRES 9 A 176 LYS ILE GLY SER ALA VAL VAL HIS GLY GLN THR GLY MET SEQRES 10 A 176 LEU LEU THR GLY SER ASN ALA LYS ALA GLN ASP LEU GLY SEQRES 11 A 176 THR ILE PRO GLY ASP ALA GLY CYS PRO TYR VAL TYR LYS SEQRES 12 A 176 LYS GLY ASN THR TRP VAL VAL ILE GLY VAL HIS VAL ALA SEQRES 13 A 176 ALA THR ARG SER GLY ASN THR VAL ILE ALA ALA THR HIS SEQRES 14 A 176 GLY GLU PRO THR LEU GLU ALA
FORMUL 2 HOH *22(H2 O)
HELIX 1 AA1 SER A 4 SER A 7 5 4 HELIX 2 AA2 HIS A 30 ALA A 32 5 3 HELIX 3 AA3 ILE A 135 ALA A 139 5 5
SHEET 1 AA1 5 VAL A 9 PHE A 12 0 SHEET 2 AA1 5 GLY A 15 TRP A 19 -1 O GLY A 15 N PHE A 12 SHEET 3 AA1 5 VAL A 24 ALA A 28 -1 O ILE A 26 N PHE A 18 SHEET 4 AA1 5 PHE A 55 PHE A 60 -1 O TYR A 58 N PHE A 25 SHEET 5 AA1 5 PHE A 47 SER A 52 -1 N THR A 50 O LYS A 57 SHEET 1 AA2 8 VAL A 72 LEU A 73 0 SHEET 2 AA2 8 THR A 150 ALA A 160 1 O VAL A 153 N VAL A 72 SHEET 3 AA2 8 THR A 166 ALA A 170 -1 O ILE A 168 N ALA A 159 SHEET 4 AA2 8 ALA A 112 LEU A 121 -1 N GLY A 119 O VAL A 167 SHEET 5 AA2 8 MET A 94 ILE A 109 -1 N GLY A 102 O THR A 118 SHEET 6 AA2 8 VAL A 82 LYS A 88 -1 N VAL A 87 O LEU A 95 SHEET 7 AA2 8 PRO A 142 LYS A 147 -1 O VAL A 144 N SER A 84 SHEET 8 AA2 8 THR A 150 ALA A 160 -1 O THR A 150 N LYS A 147
CRYST1 88.190 35.360 52.810 90.00 105.98 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 0.011339 0.000000 0.003247 0.00000
SCALE2 0.000000 0.028281 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019697 0.00000