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Yorodumi- PDB-1d9z: CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d9z | ||||||
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Title | CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP | ||||||
Components | EXCINUCLEASE UVRABC COMPONENT UVRB | ||||||
Keywords | GENE REGULATION / ATP-bound protein / EXCINUCLEASE | ||||||
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 caldotenax (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å | ||||||
Authors | Theis, K. / Chen, P.J. / Skorvaga, M. / Van Houten, B. / Kisker, C. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair. Authors: Theis, K. / Chen, P.J. / Skorvaga, M. / Van Houten, B. / Kisker, C. #1: Journal: Embo J. / Year: 1999 Title: Strand opening by the UvrA2B complex allows dynamic recognition of DNA damage Authors: Zou, Y. / Van Houten, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d9z.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d9z.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 1d9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d9z ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d9z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75429.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus caldotenax (bacteria) / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P56981 | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Chemical | ChemComp-ATP / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 9, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→20 Å / Num. all: 19075 / Num. obs: 19075 / % possible obs: 100 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 3.15→3.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.48 / Num. unique all: 2669 / % possible all: 100 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
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Refinement | Resolution: 3.15→20 Å / σ(F): -1000 / σ(I): -1000 / Stereochemistry target values: Engh & Huber / Details: maximum likelyhood
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Refinement step | Cycle: LAST / Resolution: 3.15→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'REFMAC AND XPLOR' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.262 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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