+Open data
-Basic information
Entry | Database: PDB / ID: 2zj5 | ||||||
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Title | Archaeal DNA helicase Hjm complexed with ADP in form 1 | ||||||
Components | Putative ski2-type helicase | ||||||
Keywords | HYDROLASE / RecA fold / ATP-binding / Helicase / Nucleotide-binding | ||||||
Function / homology | Function and homology information DNA 3'-5' helicase / 3'-5' DNA helicase activity / isomerase activity / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Oyama, T. / Oka, H. / Fujikane, R. / Ishino, Y. / Morikawa, K. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2009 Title: Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm Authors: Oyama, T. / Oka, H. / Mayanagi, K. / Shirai, T. / Matoba, K. / Fujikane, R. / Ishino, Y. / Morikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zj5.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zj5.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/2zj5 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/2zj5 | HTTPS FTP |
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-Related structure data
Related structure data | 2zj2SC 2zj8C 2zjaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 82746.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: O73946, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ADP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.6M ammonium sulfate, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 31108 / Num. obs: 30860 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.384 / Num. unique all: 3066 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZJ2 Resolution: 2.4→43.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 306508.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.4806 Å2 / ksol: 0.377022 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→43.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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