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Yorodumi- PDB-1yd6: Crystal structure of the GIY-YIG N-terminal endonuclease domain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yd6 | ||||||
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Title | Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Bacillus caldotenax | ||||||
Components | UvrCUvrABC endonuclease | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus caldotenax (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Truglio, J.J. / Rhau, B. / Croteau, D.L. / Wang, L. / Skorvaga, M. / Karakas, E. / DellaVecchia, M.J. / Wang, H. / Van Houten, B. / Kisker, C. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structural insights into the first incision reaction during nucleotide excision repair Authors: Truglio, J.J. / Rhau, B. / Croteau, D.L. / Wang, L. / Skorvaga, M. / Karakas, E. / Dellavecchia, M.J. / Wang, H. / Van Houten, B. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yd6.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yd6.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/1yd6 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/1yd6 | HTTPS FTP |
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-Related structure data
Related structure data | 1yczC 1yd0C 1yd1C 1yd2C 1yd3C 1yd4C 1yd5C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11471.286 Da / Num. of mol.: 4 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus caldotenax (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KWH6*PLUS #2: Chemical | #3: Chemical | #4: 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: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: Ammonium Sulfate, DTT, Sodium Acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003 | ||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. all: 29029 / Num. obs: 29029 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | ||||||||||||||||||||
Reflection shell | Resolution: 2→2.08 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.209 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.186 / ESU R Free: 0.172 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.111 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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