+Open data
-Basic information
Entry | Database: PDB / ID: 2nrv | ||||||
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Title | Crystal structure of the C-terminal half of UvrC | ||||||
Components | UvrABC system protein C | ||||||
Keywords | HYDROLASE / uvrC / RNAse H / endonuclase / helix hairpin helix / UvrABC / NER | ||||||
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: 1.8 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 | 2nrv.cif.gz | 201.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nrv.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 2nrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nrv ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nrv | HTTPS FTP |
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-Related structure data
Related structure data | 2nrrSC 2nrtC 2nrwC 2nrxC 2nrzC 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 andonuclase and helix hairpin helix domains (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 | ChemComp-NA / | #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: 2.19 Å3/Da / Density % sol: 43.92 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 15% PEG 3000, 0.1 M CHES (pH 9.5), 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 15, 2005 | |||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.0047 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.8→40 Å / Num. all: 42358 / Num. obs: 42358 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.044 / Χ2: 1.118 / Net I/σ(I): 15.8 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.351 / Num. unique all: 4187 / Χ2: 1.18 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2NRR Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.363 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.144 / 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: 31.033 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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