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Yorodumi- PDB-3bvs: Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bvs | ||||||
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Title | Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD | ||||||
Components | Alkylpurine DNA Glycosylase AlkD | ||||||
Keywords | HYDROLASE / DNA glycosylase / HEAT repeat / alkylpurine / DNA repair | ||||||
Function / homology | Leucine-rich Repeat Variant - #90 / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / metal ion binding / DNA alkylation repair protein Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Rubinson, E.H. / Eichman, B.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: A New Protein Architecture for Processing Alkylation Damaged DNA: The Crystal Structure of DNA Glycosylase AlkD. Authors: Rubinson, E.H. / Metz, A.H. / O'Quin, J. / Eichman, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bvs.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bvs.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bvs_validation.pdf.gz | 422 KB | Display | wwPDB validaton report |
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Full document | 3bvs_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 3bvs_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 3bvs_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/3bvs ftp://data.pdbj.org/pub/pdb/validation_reports/bv/3bvs | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28423.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: AlkD / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q816E8 |
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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: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 85 mM HEPES pH 7.5, 15% PEG 4000, 17% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 17, 2006 / Details: Oxford Danfysik toroidal focusing mirror |
Radiation | Monochromator: Si(111) Kohzu HLD-8NE double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→29.5 Å / Num. all: 19887 / Num. obs: 19887 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.08→2.08 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.531 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 13.711 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.956 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.213 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 25.6017 Å / Origin y: 8.9621 Å / Origin z: 0.0168 Å
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