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Yorodumi- PDB-7bih: Crystal structure of RecJ-Cdc45 from Methanothermobacter Thermoau... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bih | ||||||
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Title | Crystal structure of RecJ-Cdc45 from Methanothermobacter Thermoautotrophicus in the closed state. | ||||||
Components | Conserved proteinConservation | ||||||
Keywords | DNA BINDING PROTEIN / phosphodiesterase / dna binding / cdc45 homologue | ||||||
Function / homology | Function and homology information exonuclease activity / nucleic acid binding / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | De March, M. / Onesti, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of RecJ-Cdc45 from Methanothermobacter Thermoautotrophicus Authors: De March, M. / Onesti, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bih.cif.gz | 172.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bih.ent.gz | 132.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/7bih ftp://data.pdbj.org/pub/pdb/validation_reports/bi/7bih | HTTPS FTP |
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-Related structure data
Related structure data | 7bhiC 6tvvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 13 - 454 / Label seq-ID: 13 - 454
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-Components
#1: Protein | Mass: 50721.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH_1422 / Production host: Escherichia coli (E. coli) / References: UniProt: O27473 #2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris/HCl pH 8.5, 27% w/v PEG 4000, 0.2M MgCl2*6H20, 1mM MnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→41.5 Å / Num. obs: 19632 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.99 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 3→3.16 Å / Num. unique obs: 2851 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TVV Resolution: 3→41.3 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.88 / SU B: 24.25 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.1 Å2 / Biso mean: 69.296 Å2 / Biso min: 17.82 Å2
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Refinement step | Cycle: final / Resolution: 3→41.3 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 40410 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0
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