+Open data
-Basic information
Entry | Database: PDB / ID: 2nrt | ||||||
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Title | Crystal structure of the C-terminal half of UvrC | ||||||
Components | UvrABC system protein C | ||||||
Keywords | HYDROLASE / UvrC / endonuclease / RNAse H / helix hairpin helix / NER / UvrABC | ||||||
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: 1.5 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 | 2nrt.cif.gz | 107.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nrt.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nrt ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nrt | HTTPS FTP |
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-Related structure data
Related structure data | 2nrrSC 2nrvC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25386.404 Da / Num. of mol.: 1 Fragment: RNAse H endonuclease 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 (DE3)-RIL / References: UniProt: Q9WYA3 | ||
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#2: Chemical | ChemComp-CL / #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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG 8000, 0.1 M HEPES (pH 7.5), 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: Jan 15, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. all: 37576 / Num. obs: 37576 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Χ2: 1.13 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.417 / Num. unique all: 3672 / Χ2: 1.092 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2NRR Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.865 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.08 / 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: 25.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.502→1.54 Å / Total num. of bins used: 20
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