+Open data
-Basic information
Entry | Database: PDB / ID: 1d9x | ||||||
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Title | CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB | ||||||
Components | EXCINUCLEASE UVRABC COMPONENT UVRB | ||||||
Keywords | GENE REGULATION / apo protein | ||||||
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: 2.6 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 | 1d9x.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d9x.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 1d9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/1d9x ftp://data.pdbj.org/pub/pdb/validation_reports/d9/1d9x | 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: 75500.953 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 | #3: 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: 3.43 Å3/Da / Density % sol: 45.6879 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 8 mg/ml UvrB, 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: X25 / Wavelength: 1.1 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Sep 7, 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: 2.6→20 Å / Num. all: 32030 / Num. obs: 32030 / % possible obs: 100 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 29.4 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 7 % / Rmerge(I) obs: 0.55 / % possible all: 100 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å / σ(F): -1000 / σ(I): -1000 / Stereochemistry target values: Engh & Huber / Details: maximum likelyhood
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM | |||||||||||||||||||||||||
Software | *PLUS Name: 'REFMAC AND XPLOR' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): -1000 / % reflection Rfree: 5 % / Rfactor obs: 0.256 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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