HEADER HYDROLASE 07-MAY-09 2WHX TITLE A SECOND CONFORMATION OF THE NS3 PROTEASE-HELICASE FROM TITLE 2 DENGUE VIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE PROTEASE/NTPASE/HELICASE NS3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1475-2092; COMPND 5 SYNONYM: THE NS3 PROTEASE-HELICASE FROM DENGUE VIRUS, COMPND 6 NON-STRUCTURAL PROTEIN 3, SERINE PROTEASE SUBUNIT NS3, SERINE COMPND 7 PROTEASE SUBUNIT NS3, NON-STRUCTURAL PROTEIN 3; COMPND 8 EC: 3.4.21.91, 3.6.1.15, 3.6.1.-; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: SERINE PROTEASE SUBUNIT NS2B; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: RESIDUES 1393-1406; COMPND 14 SYNONYM: THE NS3 PROTEASE-HELICASE FROM DENGUE VIRUS, COMPND 15 NON-STRUCTURAL PROTEIN 2B, FLAVIVIRIN PROTEASE NS2B REGULATORY COMPND 16 SUBUNIT; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 4; SOURCE 3 ORGANISM_TAXID: 11070; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: DENGUE VIRUS 4; SOURCE 8 ORGANISM_TAXID: 11070; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION, HYDROLASE, ATP-BINDING, RETICULUM, KEYWDS 2 NUCLEOTIDYLTRANSFERASE, MULTIFUNCTIONAL ENZYME, TRANSCRIPTION KEYWDS 3 REGULATION, RIBONUCLEOPROTEIN, RNA-DIRECTED RNA POLYMERASE, RNA KEYWDS 4 REPLICATION, ENVELOPE PROTEIN, EXPDTA X-RAY DIFFRACTION AUTHOR D.LUO,J.LESCAR REVDAT 4 13-JUL-11 2WHX 1 VERSN REVDAT 3 16-JUN-10 2WHX 1 JRNL REVDAT 2 21-APR-10 2WHX 1 KEYWDS JRNL REVDAT 1 07-APR-10 2WHX 0 JRNL AUTH D.LUO,N.WEI,D.N.DOAN,P.N.PARADKAR,Y.CHONG,A.D.DAVIDSON, JRNL AUTH 2 M.KOTAKA,J.LESCAR,S.G.VASUDEVAN JRNL TITL FLEXIBILITY BETWEEN THE PROTEASE AND HELICASE DOMAINS OF JRNL TITL 2 THE DENGUE VIRUS NS3 PROTEIN CONFERRED BY THE LINKER REGION JRNL TITL 3 AND ITS FUNCTIONAL IMPLICATIONS. JRNL REF J.BIOL.CHEM. V. 285 18817 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20375022 JRNL DOI 10.1074/JBC.M109.090936 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 90.37 REMARK 3 NUMBER OF REFLECTIONS : 29746 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 + TEST SET) : 0.23031 REMARK 3 R VALUE (WORKING SET) : 0.22806 REMARK 3 FREE R VALUE : 0.27233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1555 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.204 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.261 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1365 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.280 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.273 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4693 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.709 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32 REMARK 3 B22 (A**2) : -0.21 REMARK 3 B33 (A**2) : 0.51 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : -0.17 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.363 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.255 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.187 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.322 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4826 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6542 ; 1.148 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 591 ; 5.641 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 218 ;34.239 ;22.982 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 822 ;17.323 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;15.512 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 712 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3665 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2965 ; 0.291 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4787 ; 0.556 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1861 ; 0.841 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1755 ; 1.382 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 21 A 179 REMARK 3 ORIGIN FOR THE GROUP (A): 5.8356 9.4345 -7.7627 REMARK 3 T TENSOR REMARK 3 T11: 0.5733 T22: 0.4779 REMARK 3 T33: 0.4388 T12: -0.0551 REMARK 3 T13: -0.1548 T23: 0.1212 REMARK 3 L TENSOR REMARK 3 L11: 5.0895 L22: 10.0105 REMARK 3 L33: 3.1952 L12: 4.4387 REMARK 3 L13: 1.9888 L23: 2.7215 REMARK 3 S TENSOR REMARK 3 S11: 0.3608 S12: -0.0641 S13: -0.3479 REMARK 3 S21: 1.2347 S22: -0.1693 S23: -1.1511 REMARK 3 S31: 0.2487 S32: 0.2200 S33: -0.1915 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 180 A 316 REMARK 3 ORIGIN FOR THE GROUP (A): 34.4137 3.9779 20.5006 REMARK 3 T TENSOR REMARK 3 T11: 0.0900 T22: 0.1685 REMARK 3 T33: 0.0448 T12: -0.0026 REMARK 3 T13: 0.0571 T23: 0.0246 REMARK 3 L TENSOR REMARK 3 L11: 5.2221 L22: 1.8758 REMARK 3 L33: 1.3373 L12: -0.4467 REMARK 3 L13: 0.7156 L23: -0.7662 REMARK 3 S TENSOR REMARK 3 S11: -0.0313 S12: 0.6445 S13: 0.1377 REMARK 3 S21: -0.2674 S22: -0.0499 S23: -0.2389 REMARK 3 S31: -0.0098 S32: 0.2786 S33: 0.0811 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 317 A 481 REMARK 3 ORIGIN FOR THE GROUP (A): 11.6265 -9.1607 28.9083 REMARK 3 T TENSOR REMARK 3 T11: 0.0384 T22: 0.0525 REMARK 3 T33: 0.0819 T12: 0.0262 REMARK 3 T13: 0.0255 T23: 0.0167 REMARK 3 L TENSOR REMARK 3 L11: 2.9477 L22: 2.4460 REMARK 3 L33: 2.1947 L12: 0.4239 REMARK 3 L13: 0.9638 L23: -0.4452 REMARK 3 S TENSOR REMARK 3 S11: 0.0842 S12: -0.0453 S13: -0.2319 REMARK 3 S21: 0.0308 S22: 0.0532 S23: 0.1305 REMARK 3 S31: 0.1212 S32: -0.0488 S33: -0.1374 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 482 A 618 REMARK 3 ORIGIN FOR THE GROUP (A): 33.6481 -5.5542 46.3241 REMARK 3 T TENSOR REMARK 3 T11: 0.0835 T22: 0.1189 REMARK 3 T33: 0.0942 T12: -0.0065 REMARK 3 T13: -0.0137 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.6288 L22: 7.8313 REMARK 3 L33: 2.7719 L12: 1.9082 REMARK 3 L13: -0.7908 L23: -3.0107 REMARK 3 S TENSOR REMARK 3 S11: 0.1585 S12: -0.1360 S13: -0.3595 REMARK 3 S21: 0.1199 S22: -0.3071 S23: -0.3732 REMARK 3 S31: 0.0869 S32: 0.2147 S33: 0.1486 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 49 C 62 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2852 14.7626 -4.0524 REMARK 3 T TENSOR REMARK 3 T11: 0.7662 T22: 0.5996 REMARK 3 T33: 0.4419 T12: -0.0703 REMARK 3 T13: 0.0322 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 11.5454 L22: 14.4932 REMARK 3 L33: 1.5361 L12: 11.6936 REMARK 3 L13: -1.6876 L23: -1.2629 REMARK 3 S TENSOR REMARK 3 S11: 0.5251 S12: -0.6993 S13: 0.5182 REMARK 3 S21: 1.3049 S22: -0.7231 S23: 0.3494 REMARK 3 S31: -0.2497 S32: -0.1497 S33: 0.1979 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2WHX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-09. REMARK 100 THE PDBE ID CODE IS EBI-39738. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC 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) : 0.97 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 : 31361 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.20 REMARK 200 RESOLUTION RANGE LOW (A) : 20.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.2 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 4.4 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.50 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 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 43.86000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 1 REMARK 465 GLY A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 TRP A 5 REMARK 465 ASP A 6 REMARK 465 VAL A 7 REMARK 465 PRO A 8 REMARK 465 SER A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 11 REMARK 465 ALA A 12 REMARK 465 ALA A 13 REMARK 465 GLN A 14 REMARK 465 LYS A 15 REMARK 465 ALA A 16 REMARK 465 THR A 17 REMARK 465 LEU A 18 REMARK 465 THR A 19 REMARK 465 GLU A 20 REMARK 465 SER A 62 REMARK 465 GLY A 63 REMARK 465 LYS A 117 REMARK 465 THR A 118 REMARK 465 LEU A 119 REMARK 465 THR A 120 REMARK 465 GLY A 121 REMARK 465 GLY A 153 REMARK 465 VAL A 154 REMARK 465 VAL A 155 REMARK 465 THR A 156 REMARK 465 LYS A 157 REMARK 465 SER A 158 REMARK 465 GLY A 159 REMARK 465 ASP A 160 REMARK 465 TYR A 161 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 LYS A 33 CG CD CE NZ REMARK 470 GLU A 43 CG CD OE1 OE2 REMARK 470 HIS A 60 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 61 CG CD OE1 OE2 REMARK 470 ARG A 64 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 74 CG OD1 ND2 REMARK 470 GLU A 92 CG CD OE1 OE2 REMARK 470 GLU A 93 CG CD OE1 OE2 REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 ILE A 123 CG1 CG2 CD1 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 ASP A 175 CG OD1 OD2 REMARK 470 LYS A 213 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 MET A 42 -56.60 -130.15 REMARK 500 GLU A 43 -163.16 -113.45 REMARK 500 ASP A 75 64.63 61.64 REMARK 500 LYS A 91 -9.39 77.53 REMARK 500 ILE A 171 -60.76 -93.82 REMARK 500 PRO A 174 -81.48 -70.56 REMARK 500 HIS A 194 160.52 -47.82 REMARK 500 THR A 315 133.31 -170.10 REMARK 500 PRO A 425 1.54 -66.59 REMARK 500 ASP A 436 89.94 -66.96 REMARK 500 GLU A 575 50.01 37.20 REMARK 500 ARG A 592 78.45 -151.19 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 MET A 42 23.8 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1620 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 200 OG1 REMARK 620 2 GLU A 285 OE2 84.2 REMARK 620 3 ADP A1619 O2B 89.1 172.5 REMARK 620 4 HOH A2135 O 84.7 79.1 97.0 REMARK 620 5 HOH A2136 O 94.0 95.3 88.4 174.4 REMARK 620 6 HOH A2137 O 176.4 97.4 89.1 92.4 89.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A1619 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1620 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1621 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A1622 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JLX RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH SSRNA AND ADP-VANADATE REMARK 900 RELATED ID: 2JLQ RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE STRUCTURE, APO REMARK 900 ENZYME. REMARK 900 RELATED ID: 2JLW RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH SSRNA2 REMARK 900 RELATED ID: 2JLU RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH SSRNA REMARK 900 RELATED ID: 2JLV RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH SSRNA AND AMPPNP REMARK 900 RELATED ID: 2JLR RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH AMPPNP REMARK 900 RELATED ID: 2JLS RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH ADP REMARK 900 RELATED ID: 2JLZ RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH SSRNA AND ADP REMARK 900 RELATED ID: 2JLY RELATED DB: PDB REMARK 900 DENGUE VIRUS 4 NS3 HELICASE IN COMPLEX REMARK 900 WITH SSRNA AND ADP-PHOSPHATE REMARK 900 RELATED ID: 2WZQ RELATED DB: PDB REMARK 900 INSERTION MUTANT E173GP174 OF THE NS3 REMARK 900 PROTEASE-HELICASE FROM DENGUE VIRUS DBREF 2WHX A 1 618 UNP Q2YHF0 POLG_DEN4T 1475 2092 DBREF 2WHX C 49 62 UNP Q2YHF0 POLG_DEN4T 1393 1406 SEQADV 2WHX LYS A 143 UNP Q2YHF0 ARG 1617 CONFLICT SEQADV 2WHX ASP A 250 UNP Q2YHF0 GLU 1724 CONFLICT SEQADV 2WHX CYS A 292 UNP Q2YHF0 SER 1766 CONFLICT SEQADV 2WHX SER A 321 UNP Q2YHF0 THR 1795 CONFLICT SEQADV 2WHX ARG A 381 UNP Q2YHF0 LYS 1855 CONFLICT SEQADV 2WHX LYS A 480 UNP Q2YHF0 ARG 1954 CONFLICT SEQRES 1 A 618 SER GLY ALA LEU TRP ASP VAL PRO SER PRO ALA ALA ALA SEQRES 2 A 618 GLN LYS ALA THR LEU THR GLU GLY VAL TYR ARG ILE MET SEQRES 3 A 618 GLN ARG GLY LEU PHE GLY LYS THR GLN VAL GLY VAL GLY SEQRES 4 A 618 ILE HIS MET GLU GLY VAL PHE HIS THR MET TRP HIS VAL SEQRES 5 A 618 THR ARG GLY SER VAL ILE CYS HIS GLU SER GLY ARG LEU SEQRES 6 A 618 GLU PRO SER TRP ALA ASP VAL ARG ASN ASP MET ILE SER SEQRES 7 A 618 TYR GLY GLY GLY TRP ARG LEU GLY ASP LYS TRP ASP LYS SEQRES 8 A 618 GLU GLU ASP VAL GLN VAL LEU ALA ILE GLU PRO GLY LYS SEQRES 9 A 618 ASN PRO LYS HIS VAL GLN THR LYS PRO GLY LEU PHE LYS SEQRES 10 A 618 THR LEU THR GLY GLU ILE GLY ALA VAL THR LEU ASP PHE SEQRES 11 A 618 LYS PRO GLY THR SER GLY SER PRO ILE ILE ASN LYS LYS SEQRES 12 A 618 GLY LYS VAL ILE GLY LEU TYR GLY ASN GLY VAL VAL THR SEQRES 13 A 618 LYS SER GLY ASP TYR VAL SER ALA ILE THR GLN ALA GLU SEQRES 14 A 618 ARG ILE GLY GLU PRO ASP TYR GLU VAL ASP GLU ASP ILE SEQRES 15 A 618 PHE ARG LYS LYS ARG LEU THR ILE MET ASP LEU HIS PRO SEQRES 16 A 618 GLY ALA GLY LYS THR LYS ARG ILE LEU PRO SER ILE VAL SEQRES 17 A 618 ARG GLU ALA LEU LYS ARG ARG LEU ARG THR LEU ILE LEU SEQRES 18 A 618 ALA PRO THR ARG VAL VAL ALA ALA GLU MET GLU GLU ALA SEQRES 19 A 618 LEU ARG GLY LEU PRO ILE ARG TYR GLN THR PRO ALA VAL SEQRES 20 A 618 LYS SER ASP HIS THR GLY ARG GLU ILE VAL ASP LEU MET SEQRES 21 A 618 CYS HIS ALA THR PHE THR THR ARG LEU LEU SER SER THR SEQRES 22 A 618 ARG VAL PRO ASN TYR ASN LEU ILE VAL MET ASP GLU ALA SEQRES 23 A 618 HIS PHE THR ASP PRO CYS SER VAL ALA ALA ARG GLY TYR SEQRES 24 A 618 ILE SER THR ARG VAL GLU MET GLY GLU ALA ALA ALA ILE SEQRES 25 A 618 PHE MET THR ALA THR PRO PRO GLY SER THR ASP PRO PHE SEQRES 26 A 618 PRO GLN SER ASN SER PRO ILE GLU ASP ILE GLU ARG GLU SEQRES 27 A 618 ILE PRO GLU ARG SER TRP ASN THR GLY PHE ASP TRP ILE SEQRES 28 A 618 THR ASP TYR GLN GLY LYS THR VAL TRP PHE VAL PRO SER SEQRES 29 A 618 ILE LYS ALA GLY ASN ASP ILE ALA ASN CYS LEU ARG LYS SEQRES 30 A 618 SER GLY LYS ARG VAL ILE GLN LEU SER ARG LYS THR PHE SEQRES 31 A 618 ASP THR GLU TYR PRO LYS THR LYS LEU THR ASP TRP ASP SEQRES 32 A 618 PHE VAL VAL THR THR ASP ILE SER GLU MET GLY ALA ASN SEQRES 33 A 618 PHE ARG ALA GLY ARG VAL ILE ASP PRO ARG ARG CYS LEU SEQRES 34 A 618 LYS PRO VAL ILE LEU THR ASP GLY PRO GLU ARG VAL ILE SEQRES 35 A 618 LEU ALA GLY PRO ILE PRO VAL THR PRO ALA SER ALA ALA SEQRES 36 A 618 GLN ARG ARG GLY ARG ILE GLY ARG ASN PRO ALA GLN GLU SEQRES 37 A 618 ASP ASP GLN TYR VAL PHE SER GLY ASP PRO LEU LYS ASN SEQRES 38 A 618 ASP GLU ASP HIS ALA HIS TRP THR GLU ALA LYS MET LEU SEQRES 39 A 618 LEU ASP ASN ILE TYR THR PRO GLU GLY ILE ILE PRO THR SEQRES 40 A 618 LEU PHE GLY PRO GLU ARG GLU LYS THR GLN ALA ILE ASP SEQRES 41 A 618 GLY GLU PHE ARG LEU ARG GLY GLU GLN ARG LYS THR PHE SEQRES 42 A 618 VAL GLU LEU MET ARG ARG GLY ASP LEU PRO VAL TRP LEU SEQRES 43 A 618 SER TYR LYS VAL ALA SER ALA GLY ILE SER TYR LYS ASP SEQRES 44 A 618 ARG GLU TRP CYS PHE THR GLY GLU ARG ASN ASN GLN ILE SEQRES 45 A 618 LEU GLU GLU ASN MET GLU VAL GLU ILE TRP THR ARG GLU SEQRES 46 A 618 GLY GLU LYS LYS LYS LEU ARG PRO LYS TRP LEU ASP ALA SEQRES 47 A 618 ARG VAL TYR ALA ASP PRO MET ALA LEU LYS ASP PHE LYS SEQRES 48 A 618 GLU PHE ALA SER GLY ARG LYS SEQRES 1 C 14 ALA ASP LEU SER LEU GLU LYS ALA ALA ASN VAL GLN TRP SEQRES 2 C 14 ASP HET ADP A1619 27 HET MN A1620 1 HET CL A1621 1 HET CL A1622 1 HETNAM MN MANGANESE (II) ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM CL CHLORIDE ION FORMUL 3 MN MN 2+ FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 CL 2(CL 1-) FORMUL 6 HOH *137(H2 O) HELIX 1 1 MET A 49 ARG A 54 1 6 HELIX 2 2 ASP A 179 ARG A 184 5 6 HELIX 3 3 ARG A 202 ARG A 214 1 13 HELIX 4 4 THR A 224 LEU A 235 1 12 HELIX 5 5 HIS A 262 SER A 272 1 11 HELIX 6 6 ASP A 290 ARG A 297 1 8 HELIX 7 7 TYR A 299 MET A 306 1 8 HELIX 8 8 PHE A 348 TYR A 354 1 7 HELIX 9 9 ASN A 369 SER A 378 1 10 HELIX 10 10 THR A 389 TYR A 394 1 6 HELIX 11 11 PRO A 395 THR A 400 1 6 HELIX 12 12 ASP A 409 MET A 413 5 5 HELIX 13 13 THR A 450 ARG A 458 1 9 HELIX 14 14 HIS A 485 ASP A 496 1 12 HELIX 15 15 GLU A 512 THR A 516 5 5 HELIX 16 16 GLU A 528 ARG A 539 1 12 HELIX 17 17 PRO A 543 ALA A 553 1 11 HELIX 18 18 ARG A 560 PHE A 564 5 5 HELIX 19 19 GLU A 567 GLN A 571 5 5 HELIX 20 20 ALA A 598 ASP A 603 1 6 HELIX 21 21 ASP A 603 SER A 615 1 13 SHEET 1 AA 4 THR A 34 GLN A 35 0 SHEET 2 AA 4 TYR A 23 GLN A 27 -1 O GLN A 27 N THR A 34 SHEET 3 AA 4 LEU C 51 LYS C 55 -1 O SER C 52 N MET A 26 SHEET 4 AA 4 ILE A 58 CYS A 59 1 O CYS A 59 N LEU C 53 SHEET 1 AB 3 PHE A 46 THR A 48 0 SHEET 2 AB 3 MET A 76 TYR A 79 -1 O ILE A 77 N THR A 48 SHEET 3 AB 3 TRP A 69 ASP A 71 -1 O TRP A 69 N SER A 78 SHEET 1 AC 3 LYS A 107 THR A 111 0 SHEET 2 AC 3 VAL A 95 ALA A 99 -1 O VAL A 95 N THR A 111 SHEET 3 AC 3 ILE A 139 ILE A 140 -1 O ILE A 140 N GLN A 96 SHEET 1 AD 6 LEU A 188 MET A 191 0 SHEET 2 AD 6 ALA A 310 MET A 314 1 O ALA A 311 N THR A 189 SHEET 3 AD 6 LEU A 280 ASP A 284 1 O ILE A 281 N ILE A 312 SHEET 4 AD 6 THR A 218 ALA A 222 1 O LEU A 219 N VAL A 282 SHEET 5 AD 6 VAL A 257 CYS A 261 1 O ASP A 258 N ILE A 220 SHEET 6 AD 6 ILE A 240 TYR A 242 1 O ARG A 241 N LEU A 259 SHEET 1 AE 6 ILE A 332 GLU A 336 0 SHEET 2 AE 6 ASP A 470 PHE A 474 1 O ASP A 470 N GLU A 333 SHEET 3 AE 6 VAL A 422 ASP A 424 1 O VAL A 422 N VAL A 473 SHEET 4 AE 6 THR A 358 PHE A 361 1 O VAL A 359 N ILE A 423 SHEET 5 AE 6 PHE A 404 THR A 407 1 O VAL A 405 N TRP A 360 SHEET 6 AE 6 VAL A 382 LEU A 385 1 O ILE A 383 N VAL A 406 SHEET 1 AF 2 ARG A 427 LEU A 434 0 SHEET 2 AF 2 ARG A 440 PRO A 448 -1 O ARG A 440 N LEU A 434 SHEET 1 AG 2 LEU A 573 GLU A 574 0 SHEET 2 AG 2 MET A 577 GLU A 578 -1 O MET A 577 N GLU A 574 SHEET 1 AH 2 GLU A 580 TRP A 582 0 SHEET 2 AH 2 LYS A 588 LYS A 590 -1 O LYS A 589 N ILE A 581 LINK MN MN A1620 OG1 THR A 200 1555 1555 2.34 LINK MN MN A1620 OE2 GLU A 285 1555 1555 2.15 LINK MN MN A1620 O2B ADP A1619 1555 1555 2.20 LINK MN MN A1620 O HOH A2135 1555 1555 2.13 LINK MN MN A1620 O HOH A2136 1555 1555 2.18 LINK MN MN A1620 O HOH A2137 1555 1555 2.46 CISPEP 1 MET A 42 GLU A 43 0 3.23 CISPEP 2 GLU A 43 GLY A 44 0 -0.27 CISPEP 3 LYS A 142 LYS A 143 0 0.60 CISPEP 4 LYS A 143 GLY A 144 0 0.36 CISPEP 5 GLY A 172 GLU A 173 0 1.68 CISPEP 6 GLU A 173 PRO A 174 0 -0.09 CISPEP 7 GLY A 445 PRO A 446 0 4.86 SITE 1 AC1 13 GLY A 196 ALA A 197 GLY A 198 LYS A 199 SITE 2 AC1 13 THR A 200 LYS A 201 ASN A 329 ARG A 463 SITE 3 AC1 13 MN A1620 HOH A2133 HOH A2134 HOH A2136 SITE 4 AC1 13 HOH A2137 SITE 1 AC2 6 THR A 200 GLU A 285 ADP A1619 HOH A2135 SITE 2 AC2 6 HOH A2136 HOH A2137 SITE 1 AC3 4 LYS A 199 ALA A 316 GLN A 456 HOH A2091 SITE 1 AC4 3 ILE A 365 ARG A 387 THR A 408 CRYST1 52.420 87.720 75.779 90.00 92.90 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 0.019077 0.000000 0.000966 0.00000 SCALE2 0.000000 0.011400 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013213 0.00000