+Open data
-Basic information
Entry | Database: PDB / ID: 3gva | ||||||
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Title | Crystal Structure Analysis of S. Pombe ATL | ||||||
Components | Alkyltransferase-like protein 1 | ||||||
Keywords | DNA BINDING PROTEIN / Alkylated DNA damage repair / DNA damage / DNA repair / DNA-binding | ||||||
Function / homology | Function and homology information O6-alkylguanine-DNA binding / global genome nucleotide-excision repair / transcription-coupled nucleotide-excision repair / catalytic activity / damaged DNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Tubbs, J.L. / Arvai, A.S. / Tainer, J.A. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Authors: Tubbs, J.L. / Latypov, V. / Kanugula, S. / Butt, A. / Melikishvili, M. / Kraehenbuehl, R. / Fleck, O. / Marriott, A. / Watson, A.J. / Verbeek, B. / McGown, G. / Thorncroft, M. / Santibanez- ...Authors: Tubbs, J.L. / Latypov, V. / Kanugula, S. / Butt, A. / Melikishvili, M. / Kraehenbuehl, R. / Fleck, O. / Marriott, A. / Watson, A.J. / Verbeek, B. / McGown, G. / Thorncroft, M. / Santibanez-Koref, M.F. / Millington, C. / Arvai, A.S. / Kroeger, M.D. / Peterson, L.A. / Williams, D.M. / Fried, M.G. / Margison, G.P. / Pegg, A.E. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gva.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gva.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 3gva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gva ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gva | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 13662.412 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: atl1, SPAC1250.04c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UTN9 #2: Water | ChemComp-HOH / | |
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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: 1.92 Å3/Da / Density % sol: 35.83 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 14855 / % possible obs: 98.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 2→2.7 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.286 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Resolution: 2→39.02 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 114432 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.741 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.77 Å2 / Biso mean: 34.943 Å2 / Biso min: 13.99 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→39.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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