HEADER RNA BINDING PROTEIN 07-MAY-07 2Z0M TITLE CRYSTAL STRUCTURE OF HYPOTHETICAL ATP-DEPENDENT RNA HELICASE FROM TITLE 2 SULFOLOBUS TOKODAII COMPND MOL_ID: 1; COMPND 2 MOLECULE: 337AA LONG HYPOTHETICAL ATP-DEPENDENT RNA HELICASE DEAD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS TOKODAII; SOURCE 3 ORGANISM_TAXID: 111955; SOURCE 4 STRAIN: STRAIN7; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS HELICASE, ATP-BINDING, HYDROLASE, NUCLEOTIDE-BINDING, RNA BINDING KEYWDS 2 PROTEIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 3 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 4 GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR N.NAKAGAWA,S.KUSANO,M.SHIROUZU,L.CHEN,Z.-Q.FU,J.CHRZAS,B.-C.WANG, AUTHOR 2 S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 3 INITIATIVE (RSGI) REVDAT 3 01-NOV-23 2Z0M 1 REMARK REVDAT 2 24-FEB-09 2Z0M 1 VERSN REVDAT 1 13-NOV-07 2Z0M 0 JRNL AUTH N.NAKAGAWA,S.KUSANO,M.SHIROUZU,L.CHEN,Z.-Q.FU,J.CHRZAS, JRNL AUTH 2 B.-C.WANG,S.YOKOYAMA,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF HYPOTHETICAL ATP-DEPENDENT RNA HELICASE JRNL TITL 2 FROM SULFOLOBUS TOKODAII JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 127064.470 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 33371 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) : 0.205 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3326 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4601 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 496 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.41000 REMARK 3 B22 (A**2) : 1.18000 REMARK 3 B33 (A**2) : 0.23000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.09 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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) : 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 : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 53.03 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000027370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34129 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.045 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 40.2880 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27900 REMARK 200 FOR SHELL : 5.943 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1HV8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA/K PHOSPHATE, 40% ETHYLENE REMARK 280 GLYCOL, PH 6.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.49250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.12900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.60800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.12900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.49250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.60800 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 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 LYS A 332 REMARK 465 VAL A 333 REMARK 465 SER A 334 REMARK 465 GLN A 335 REMARK 465 LYS A 336 REMARK 465 ALA A 337 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 184 66.88 28.64 REMARK 500 TRP A 208 -74.90 -154.58 REMARK 500 LEU A 321 -74.94 -96.81 REMARK 500 GLU A 323 46.52 -85.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: STO001002459.2 RELATED DB: TARGETDB DBREF 2Z0M A 1 337 UNP Q96XQ7 Q96XQ7_SULTO 1 337 SEQRES 1 A 337 MET ASN GLU LYS ILE GLU GLN ALA ILE ARG GLU MET GLY SEQRES 2 A 337 PHE LYS ASN PHE THR GLU VAL GLN SER LYS THR ILE PRO SEQRES 3 A 337 LEU MET LEU GLN GLY LYS ASN VAL VAL VAL ARG ALA LYS SEQRES 4 A 337 THR GLY SER GLY LYS THR ALA ALA TYR ALA ILE PRO ILE SEQRES 5 A 337 LEU GLU LEU GLY MET LYS SER LEU VAL VAL THR PRO THR SEQRES 6 A 337 ARG GLU LEU THR ARG GLN VAL ALA SER HIS ILE ARG ASP SEQRES 7 A 337 ILE GLY ARG TYR MET ASP THR LYS VAL ALA GLU VAL TYR SEQRES 8 A 337 GLY GLY MET PRO TYR LYS ALA GLN ILE ASN ARG VAL ARG SEQRES 9 A 337 ASN ALA ASP ILE VAL VAL ALA THR PRO GLY ARG LEU LEU SEQRES 10 A 337 ASP LEU TRP SER LYS GLY VAL ILE ASP LEU SER SER PHE SEQRES 11 A 337 GLU ILE VAL ILE ILE ASP GLU ALA ASP LEU MET PHE GLU SEQRES 12 A 337 MET GLY PHE ILE ASP ASP ILE LYS ILE ILE LEU ALA GLN SEQRES 13 A 337 THR SER ASN ARG LYS ILE THR GLY LEU PHE SER ALA THR SEQRES 14 A 337 ILE PRO GLU GLU ILE ARG LYS VAL VAL LYS ASP PHE ILE SEQRES 15 A 337 THR ASN TYR GLU GLU ILE GLU ALA CYS ILE GLY LEU ALA SEQRES 16 A 337 ASN VAL GLU HIS LYS PHE VAL HIS VAL LYS ASP ASP TRP SEQRES 17 A 337 ARG SER LYS VAL GLN ALA LEU ARG GLU ASN LYS ASP LYS SEQRES 18 A 337 GLY VAL ILE VAL PHE VAL ARG THR ARG ASN ARG VAL ALA SEQRES 19 A 337 LYS LEU VAL ARG LEU PHE ASP ASN ALA ILE GLU LEU ARG SEQRES 20 A 337 GLY ASP LEU PRO GLN SER VAL ARG ASN ARG ASN ILE ASP SEQRES 21 A 337 ALA PHE ARG GLU GLY GLU TYR ASP MET LEU ILE THR THR SEQRES 22 A 337 ASP VAL ALA SER ARG GLY LEU ASP ILE PRO LEU VAL GLU SEQRES 23 A 337 LYS VAL ILE ASN PHE ASP ALA PRO GLN ASP LEU ARG THR SEQRES 24 A 337 TYR ILE HIS ARG ILE GLY ARG THR GLY ARG MET GLY ARG SEQRES 25 A 337 LYS GLY GLU ALA ILE THR PHE ILE LEU ASN GLU TYR TRP SEQRES 26 A 337 LEU GLU LYS GLU VAL LYS LYS VAL SER GLN LYS ALA FORMUL 2 HOH *270(H2 O) HELIX 1 1 ASN A 2 MET A 12 1 11 HELIX 2 2 THR A 18 GLN A 30 1 13 HELIX 3 3 GLY A 43 GLY A 56 1 14 HELIX 4 4 THR A 65 GLY A 80 1 16 HELIX 5 5 PRO A 95 ARG A 104 1 10 HELIX 6 6 THR A 112 LYS A 122 1 11 HELIX 7 7 ASP A 126 PHE A 130 5 5 HELIX 8 8 GLU A 137 MET A 144 1 8 HELIX 9 9 PHE A 146 THR A 157 1 12 HELIX 10 10 PRO A 171 ILE A 182 1 12 HELIX 11 11 CYS A 191 ALA A 195 5 5 HELIX 12 12 TRP A 208 GLU A 217 1 10 HELIX 13 13 THR A 229 ARG A 238 1 10 HELIX 14 14 PRO A 251 GLU A 264 1 14 HELIX 15 15 THR A 273 ARG A 278 1 6 HELIX 16 16 ASP A 296 GLY A 305 1 10 HELIX 17 17 ARG A 306 THR A 307 5 2 HELIX 18 18 GLY A 308 ARG A 312 5 5 HELIX 19 19 GLU A 323 LYS A 331 1 9 SHEET 1 A 7 VAL A 87 VAL A 90 0 SHEET 2 A 7 ILE A 108 ALA A 111 1 O ILE A 108 N ALA A 88 SHEET 3 A 7 SER A 59 VAL A 62 1 N VAL A 61 O VAL A 109 SHEET 4 A 7 ILE A 132 ASP A 136 1 O ILE A 134 N VAL A 62 SHEET 5 A 7 ILE A 162 SER A 167 1 O PHE A 166 N ILE A 135 SHEET 6 A 7 VAL A 34 ARG A 37 1 N VAL A 36 O LEU A 165 SHEET 7 A 7 GLU A 186 GLU A 189 1 O ILE A 188 N ARG A 37 SHEET 1 B 6 VAL A 197 HIS A 203 0 SHEET 2 B 6 GLY A 314 ILE A 320 1 O ILE A 320 N VAL A 202 SHEET 3 B 6 LYS A 287 ASN A 290 1 N ASN A 290 O ILE A 317 SHEET 4 B 6 VAL A 223 PHE A 226 1 N ILE A 224 O ILE A 289 SHEET 5 B 6 MET A 269 THR A 272 1 O LEU A 270 N VAL A 225 SHEET 6 B 6 ALA A 243 LEU A 246 1 N ILE A 244 O ILE A 271 CRYST1 44.985 87.216 108.258 90.00 90.00 90.00 P 21 21 21 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 0.022230 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009237 0.00000