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Yorodumi- PDB-5loi: Crystal structure of Myceliophthora thermophila Rad26 (residues 3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5loi | ||||||
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Title | Crystal structure of Myceliophthora thermophila Rad26 (residues 373-841) | ||||||
Components | Rad26 | ||||||
Keywords | SIGNALING PROTEIN / Rad26 (ATRIP) / Rad3 (ATR) / DNA-damage response (DDR) / kinase signaling | ||||||
Function / homology | Rad26-like, helical repeats / : / : / Rad26-like, helical repeats / Rad26-like, C-terminal domain / Rad26-like, N-terminal domain / DNA repair protein Rad26 Function and homology information | ||||||
Biological species | Myceliophthora thermophila ATCC 42464 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.153 Å | ||||||
Authors | Andersen, K.R. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Insights into Rad3 kinase recruitment from the crystal structure of the DNA damage checkpoint protein Rad26. Authors: Andersen, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5loi.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5loi.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 5loi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5loi_validation.pdf.gz | 420.7 KB | Display | wwPDB validaton report |
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Full document | 5loi_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 5loi_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5loi_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/5loi ftp://data.pdbj.org/pub/pdb/validation_reports/lo/5loi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 51698.379 Da / Num. of mol.: 1 / Fragment: UNP residues 373-841 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myceliophthora thermophila ATCC 42464 (fungus) Gene: MYCTH_2305697 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LOBSTR / References: UniProt: G2QDY6 |
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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: 5.63 Å3/Da / Density % sol: 78.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M BIS-TRIS pH 6.5 10% (w/v) PEG 10K 0.2M Potassium sodium tartrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→105.4 Å / Num. all: 540544 / Num. obs: 20640 / % possible obs: 99.4 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.025 / Net I/σ(I): 23 |
Reflection shell | Resolution: 3.15→3.27 Å / Redundancy: 26.8 % / Rmerge(I) obs: 4.781 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1932 / CC1/2: 0.612 / Rpim(I) all: 0.937 / % possible all: 95.07 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.153→105.391 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.153→105.391 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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