HEADER PROTEASE 14-MAY-98 1BEF OBSLTE 08-DEC-09 1BEF TITLE CRYSTAL STRUCTURE OF DENGUE VIRUS NS3 SERINE PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DENGUE VIRUS NS3 SERINE PROTEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PROTEASE DOMAIN, RESIDUES 1 - 183; COMPND 5 SYNONYM: NS3-PRO; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 2; SOURCE 3 ORGANISM_TAXID: 11060; SOURCE 4 STRAIN: NEW GUINEA; SOURCE 5 VARIANT: 2; SOURCE 6 CELL_LINE: XL1-BLUE; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE MRF' KEYWDS PROTEASE, TRYPSIN-LIKE, VIRAL-MATURATION EXPDTA X-RAY DIFFRACTION AUTHOR H.M.K.MURTHY,S.CLUM,R.PADMANABHAN REVDAT 4 25-APR-12 1BEF 1 REMARK REVDAT 3 08-DEC-09 1BEF 1 OBSLTE REVDAT 2 24-FEB-09 1BEF 1 VERSN REVDAT 1 18-MAY-99 1BEF 0 JRNL AUTH H.M.MURTHY,S.CLUM,R.PADMANABHAN JRNL TITL RETRACTED BY PUBLISHER JRNL REF J.BIOL.CHEM. V. 284 34468 2009 JRNL REFN ISSN 0021-9258 JRNL DOI 10.1074/JBC.A005573200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.M.MURTHY,S.CLUM,R.PADMANABHAN REMARK 1 TITL DENGUE VIRUS NS3 SERINE PROTEASE. CRYSTAL STRUCTURE AND REMARK 1 TITL 2 INSIGHTS INTO INTERACTION OF THE ACTIVE SITE WITH SUBSTRATES REMARK 1 TITL 3 BY MOLECULAR MODELING AND STRUCTURAL ANALYSIS OF MUTATIONAL REMARK 1 TITL 4 EFFECTS. REMARK 1 REF J.BIOL.CHEM. V. 274 5573 1999 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10026173 REMARK 1 DOI 10.1074/JBC.274.9.5573 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.8 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0001 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.7 REMARK 3 NUMBER OF REFLECTIONS : 12838 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1283 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2120 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 212 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1336 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.60 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.240 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.530 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.600 ; 2.500 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 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 5 REMARK 5 THE ENTRY IS OBSOLETED DUE TO PAPER RETRACTION REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.8 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 31.20000 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 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 ALA A 1 REMARK 465 GLY A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 4 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 CE MET A 49 O TYR A 150 2.11 REMARK 500 O GLU A 94 NZ LYS A 142 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE LYS A 15 O LYS A 90 1455 1.78 REMARK 500 CD LYS A 15 O LYS A 90 1455 1.81 REMARK 500 CB ALA A 22 OD2 ASP A 129 2646 2.07 REMARK 500 CB ALA A 22 CG ASP A 129 2646 2.12 REMARK 500 CB SER A 158 O HOH A 212 2656 2.15 REMARK 500 CD ARG A 157 O HOH A 196 2657 2.18 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 LYS A 26 36.24 39.62 REMARK 500 GLN A 27 -168.23 -128.14 REMARK 500 LYS A 28 91.94 85.14 REMARK 500 SER A 34 -57.64 -159.56 REMARK 500 ARG A 54 43.81 39.57 REMARK 500 ARG A 157 -17.95 72.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLN A 110 24.5 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CIC REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL DBREF 1BEF A 1 181 UNP Q9Q4T1 Q9Q4T1_9FLAV 433 613 SEQADV 1BEF ILE A 149 UNP Q9Q4T1 LEU 581 CONFLICT SEQRES 1 A 181 ALA GLY VAL LEU TRP ASP VAL PRO SER PRO PRO PRO VAL SEQRES 2 A 181 GLY LYS ALA GLU LEU GLU ASP GLY ALA TYR ARG ILE LYS SEQRES 3 A 181 GLN LYS GLY ILE LEU GLY TYR SER GLN ILE GLY ALA GLY SEQRES 4 A 181 VAL TYR LYS GLU GLY THR PHE HIS THR MET TRP HIS VAL SEQRES 5 A 181 THR ARG GLY ALA VAL LEU MET HIS LYS GLY LYS ARG ILE SEQRES 6 A 181 GLU PRO SER TRP ALA ASP VAL LYS LYS ASP LEU VAL SER SEQRES 7 A 181 CYS GLY GLY GLY TRP LYS LEU GLU GLY GLU TRP LYS GLU SEQRES 8 A 181 GLY GLU GLU VAL GLN VAL LEU ALA LEU GLU PRO GLY LYS SEQRES 9 A 181 ASN PRO ARG ALA VAL GLN THR LYS PRO GLY LEU PHE LYS SEQRES 10 A 181 THR ASN ALA GLY THR ILE GLY ALA VAL SER LEU ASP PHE SEQRES 11 A 181 SER PRO GLY THR SER GLY SER PRO ILE ILE ASP LYS LYS SEQRES 12 A 181 GLY LYS VAL VAL GLY ILE TYR GLY ASN GLY VAL VAL THR SEQRES 13 A 181 ARG SER GLY ALA TYR VAL SER ALA ILE ALA GLN THR GLU SEQRES 14 A 181 LYS SER ILE GLU ASP ASN PRO GLU ILE GLU ASP ASP FORMUL 2 HOH *64(H2 O) HELIX 1 1 PRO A 10 ALA A 16 1 7 HELIX 2 2 THR A 168 SER A 171 1 4 SHEET 1 A 2 VAL A 95 LEU A 98 0 SHEET 2 A 2 PRO A 138 ASP A 141 -1 N ILE A 140 O GLN A 96 SHEET 1 B 3 LYS A 112 GLY A 114 0 SHEET 2 B 3 ALA A 160 ALA A 164 -1 N SER A 163 O PRO A 113 SHEET 3 B 3 ASN A 152 VAL A 155 -1 N VAL A 154 O TYR A 161 SITE 1 CIC 1 HIS A 51 CRYST1 48.800 62.400 39.600 90.00 96.70 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 0.020492 0.000000 0.002407 0.00000 SCALE2 0.000000 0.016026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025426 0.00000