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Yorodumi- PDB-3fhf: Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fhf | ||||||
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Title | Crystal structure of Methanocaldococcus jannaschii 8-oxoguanine DNA glycosylase (MjOgg) | ||||||
Components | N-glycosylase/DNA lyase | ||||||
Keywords | DNA repair / HYDROLASE / LYASE / ogg / helix-hairpin-helix / glycosylase / 8-oxoguanine / 8-oxoG / MjOgg / DNA damage / Glycosidase / Multifunctional enzyme / Nuclease | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing N-glycosyl compounds / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.995 Å | ||||||
Authors | Faucher, F. / Doublie, S. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Crystal structures of two archaeal 8-oxoguanine DNA glycosylases provide structural insight into guanine/8-oxoguanine distinction. Authors: Faucher, F. / Duclos, S. / Bandaru, V. / Wallace, S.S. / Doublie, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fhf.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fhf.ent.gz | 45.3 KB | Display | PDB format |
PDBx/mmJSON format | 3fhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fhf_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 3fhf_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 3fhf_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3fhf_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/3fhf ftp://data.pdbj.org/pub/pdb/validation_reports/fh/3fhf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25825.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: 1451601, MJ0724, ogg / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS References: UniProt: Q58134, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase |
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#2: 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: 2.21 Å3/Da / Density % sol: 44.27 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: PEG 4000 30%, 0.1M sodium citrate, 1% b-Mercaptoethanol, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9794, 0.9796, 0.97166 | ||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2008 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings | ||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.995→19.56 Å / Num. all: 29750 / Num. obs: 28691 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.084 / Net I/σ(I): 15.43 | ||||||||||||
Reflection shell | Resolution: 1.995→2.1 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 8.23 / Num. unique all: 4041 / Rsym value: 0.279 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Resolution: 1.995→19.56 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2736238 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: 1. The Friedel pairs were used in phasing. 2. BULK SOLVENT MODEL USED in refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.01 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.48 Å2 / Biso mean: 24.682 Å2 / Biso min: 7.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.995→19.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.995→2.13 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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