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- PDB-2z41: Crystal Structure Analysis of the Ski2-type RNA helicase -

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Basic information

Entry
Database: PDB / ID: 2z41
TitleCrystal Structure Analysis of the Ski2-type RNA helicase
Componentsputative ski2-type helicase
KeywordsHYDROLASE / RNA helicase / DNA helicase
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.51 Å
AuthorsNakashima, T. / Zhang, X. / Kakuta, Y. / Yao, M. / Tanaka, I. / Kimura, M.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3
Authors: Zhang, X. / Nakashima, T. / Kakuta, Y. / Yao, M. / Tanaka, I. / Kimura, M.
History
DepositionJun 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / database_2 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative ski2-type helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1902
Polymers55,1661
Non-polymers241
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.7370, 133.7370, 133.6360
Angle α, β, γ (deg.)90, 90, 90
Int Tables number95
Space group name H-MP4322
DetailsThe biological unit is not determined. It may be a monomer.

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Components

#1: Protein putative ski2-type helicase / Coordinate model: Cα atoms only


Mass: 55166.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1280 / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Sequence detailsBECAUSE THE ELECTRON DENSITY WAS POOR, THE SIDE CHAINS WERE PARTIALLY FITTED BY A HOMOLOGY MODEL ...BECAUSE THE ELECTRON DENSITY WAS POOR, THE SIDE CHAINS WERE PARTIALLY FITTED BY A HOMOLOGY MODEL MADE FROM RECQ PROTEIN (PDB ID: 1OYW). ALTHOUGH REFINEMENT WAS PERFORMED BY THE MODEL CONTAINING A PART OF SIDE CHAINS OF PROTEIN, AMINO ACID SEQUENCE COULD NOT ASSIGNED IN THIS ENTRY. RESIDUE NUMBERING IS ARBITRARY, NOT CORRESPONDING TO THE ONE IN UNIPROT ENTRY, O59025. THE FOLLOWING IS THE ONE-LETTER SEQUENCE FOR THE PROTEIN MODELED IN THIS STRUCTURE, UNIPROT ENTRY O59025: MKVEELRIDE RIKEVLKKRG ISELYPPQAE ALTSGILKGE NALIAIPTAS GKTLIAEIAI VNRLLKEGGK AVYLVPLKAL AEEKFKEFKD WEELGLKVAM ATGDYDSKDE WLGGYDIIIA TAEKFDSLLR HGSSWIRNVK VLVVDEIHLI GSRDRGATLE FIITQMLNRA QIIGLSATIG NPEELAEWLN AKLIKSDWRP VKLRRGVFYQ GFVFWEDGKT EKFNSWEELV YDAIKRSKGS LVFVNMRRKA EKTALELSKK IRNFLTKKEL RELKELAESL EENPTNEKLA KALQGGVAFH HAGLGREERV LVEENFKKGL IKVVVATPTL SAGINTPAFR VIVRDTWRYS EFGMERIPIL EIQQMMGRAG RPKYDEVGEA IIVSTTEEPS TVMERYIKGK PEKLFSQLSN ESILRGQILA LIATFNFSSF REIYDFLERT FYAYQGKDPY TLEDRIRDIV YFLLENEFIE ITLDDEIKAL PLGIRTAKLY IDPMTAKIFK DTLPKIEKDP NPLGILHVIS LTPDLIPLPY GKKELPMLED EYYSFKDRLY FELDWEDERK FLRAFKTALV LNAWINEVPE GEIVEKFNVE PGDIYRIVET AEWLVYSLKE IAKTLEYSQD VINYLETLRV RVKHGIREEL IPLMELPMIG RKRARALYNA GFRDLESIKN ARPAELLEVE GIGAKIVEAI LKHLGREVKI VQKPRKGTLD YYLHPAAALE HHHHHH THE RESIDUES, AAALEHHHHHH, AT THE C-TERMINAL ARE EXPRESSION TAGS. IN ADDITION, ALL METS IN THIS PROTEIN WERE ENGINEERED TO MSE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 10% 2-propanol, 0.2M Lithium sulfate, 0.1M phosphate-citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 3.51→50 Å / Num. all: 16159 / Num. obs: 16159 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.137
Reflection shellResolution: 3.51→3.63 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.454 / Num. unique all: 2969 / Rsym value: 0.474 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.51→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The R factor and free-R factor were calculated for the coordinates containing the side chains.
RfactorNum. reflection% reflectionSelection details
Rfree0.3438 770 -RANDOM
Rwork0.2911 ---
obs-14464 94.9 %-
Refinement stepCycle: LAST / Resolution: 3.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms648 0 1 0 649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011297
X-RAY DIFFRACTIONc_angle_deg2.16166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
3.51-3.560.4044380.3832X-RAY DIFFRACTION8956
3.56-3.60.38570.3905X-RAY DIFFRACTION8946
3.6-3.650.4786400.4274X-RAY DIFFRACTION9396
3.65-3.70.3989550.3983X-RAY DIFFRACTION9666
3.7-3.750.4133570.4093X-RAY DIFFRACTION9506
3.75-3.810.4091440.388X-RAY DIFFRACTION9346

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