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Yorodumi- PDB-3dtk: Crystal structure of the IRRE protein, a central regulator of DNA... -
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-Basic information
Entry | Database: PDB / ID: 3dtk | ||||||
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Title | Crystal structure of the IRRE protein, a central regulator of DNA damage repair in deinococcaceae | ||||||
Components | IRRE PROTEIN | ||||||
Keywords | GENE REGULATION / IrrE / Deinococcus / Radiotolerance / Metallopeptidase | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metallopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | deinococcus deserti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å | ||||||
Authors | Vujicic-Zagar, A. / Dulermo, R. / Le Gorrec, M. / Vannier, F. / Servant, P. / Sommer, S. / de Groot, A. / Serre, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure of the IrrE protein, a central regulator of DNA damage repair in deinococcaceae Authors: Vujicic-Zagar, A. / Dulermo, R. / Le Gorrec, M. / Vannier, F. / Servant, P. / Sommer, S. / de Groot, A. / Serre, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dtk.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dtk.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dtk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dtk_validation.pdf.gz | 433.5 KB | Display | wwPDB validaton report |
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Full document | 3dtk_full_validation.pdf.gz | 444.6 KB | Display | |
Data in XML | 3dtk_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3dtk_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/3dtk ftp://data.pdbj.org/pub/pdb/validation_reports/dt/3dtk | HTTPS FTP |
-Related structure data
Related structure data | 3dteSC 3dtiC 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: 32337.150 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) deinococcus deserti (bacteria) / Gene: irrE / Plasmid: PET-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B5B9W8, UniProt: C1CZ84*PLUS | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | Nonpolymer details | ZINC HAS BEEN INTRODUCED BY SOAKING THE NATIVE CRYSTALS INTO 10MM ZNSO4 FOR 2 MINUTES. ONE CHLORIDE ...ZINC HAS BEEN INTRODUCED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion / pH: 7.5 Details: 20% PEG 3350, 0.2M Potassium fluoride, pH 7.5, VAPOR DIFFUSION, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.24→40 Å / Num. obs: 4827 / % possible obs: 97.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 89 Å2 / Rsym value: 0.095 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 3.24→3.42 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.598 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DTE Resolution: 3.24→19.83 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.883 / SU B: 26.06 / SU ML: 0.424 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / 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: 75.982 Å2
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Refinement step | Cycle: LAST / Resolution: 3.24→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.24→3.322 Å / Total num. of bins used: 20
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