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Yorodumi- PDB-2nrz: Crystal structure of the C-terminal half of UvrC bound to its cat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nrz | ||||||
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Title | Crystal structure of the C-terminal half of UvrC bound to its catalytic divalent cation | ||||||
Components | UvrABC system protein C | ||||||
Keywords | HYDROLASE / uvrC / RNAse H / endonuclase / helix hairpin helix / UvrABC / NER / divalent cation / manganese | ||||||
Function / homology | Function and homology information excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / DNA damage response / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Karakas, E. / Truglio, J.J. / Kisker, C. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad. Authors: Karakas, E. / Truglio, J.J. / Croteau, D. / Rhau, B. / Wang, L. / 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 | 2nrz.cif.gz | 189.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nrz.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nrz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nrz ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nrz | HTTPS FTP |
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-Related structure data
Related structure data | 2nrrSC 2nrtC 2nrvC 2nrwC 2nrxC S: Starting model for refinement 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
#1: Protein | Mass: 25386.404 Da / Num. of mol.: 2 Fragment: The RNAse H endonuclase and helix hairpin helix domains of UvrC (residues 339-557) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: uvrC / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (CE3)-RIL / References: UniProt: Q9WYA3 #2: Chemical | #3: 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: 2.9 Å3/Da / Density % sol: 57.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% PEG 8000, 0.1 M HEPES (pH 7.5), 0.01 M manganese chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.009 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 76400 / Num. obs: 38877 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.065 / Χ2: 1.208 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.424 / Num. unique all: 7612 / Χ2: 1.001 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2NRR Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.33 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.152 / 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: 34.633 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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