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Yorodumi- PDB-2d7d: Structural insights into the cryptic DNA dependent ATP-ase activi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d7d | ||||||
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Title | Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB | ||||||
Components |
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Keywords | HYDROLASE/DNA / Helicase / Protein-DNA-ADP ternary complex / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Barrett, T.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural insights into the cryptic DNA-dependent ATPase activity of UvrB Authors: Eryilmaz, J. / Ceschini, S. / Ryan, J. / Geddes, S. / Waters, T.R. / Barrett, T.E. #1: Journal: To be Published Title: Structural insights into the cryptic ATP-ase activity of UvrB Authors: Eryilmaz, J. / Ceschini, S. / Ryan, J. / Geddes, S. / Waters, T.R. / Barrett, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d7d.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d7d.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/2d7d ftp://data.pdbj.org/pub/pdb/validation_reports/d7/2d7d | HTTPS FTP |
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-Related structure data
Related structure data | 1d9xS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly consists of a full UvrB monomer, a trithymine oligonucleotide, a single molecule of ADP and a helix-loop-helix dimer fragment resulting from proteolysis of UvrB. |
-Components
#1: DNA chain | Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | Mass: 76440.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: uvrB / Plasmid: pET 8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS References: UniProt: P37954, Hydrolases; Acting on ester bonds |
#3: Protein/peptide | Mass: 4692.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: uvrB / Plasmid: pET 8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS References: UniProt: P37954, Hydrolases; Acting on ester bonds |
#4: Chemical | ChemComp-ADP / |
#5: 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: 2.12 Å3/Da / Density % sol: 41.98 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: microbatch / pH: 8.5 Details: 18-20% (w/v) PEG 10000 0.1M Tris-Hcl, pH 8.5, Microbatch, temperature 289K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 22, 2005 / Details: Mirrors |
Radiation | Monochromator: Si 111 channel-cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 39593 / Num. obs: 39593 / % possible obs: 96.1 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Redundancy: 5.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5487 / Rsym value: 0.31 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D9X Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 7.237 / SU ML: 0.186 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 23.146 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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