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Yorodumi- PDB-4q10: The catalytic core of Rad2 in complex with DNA substrate (complex IV) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q10 | ||||||
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Title | The catalytic core of Rad2 in complex with DNA substrate (complex IV) | ||||||
Components |
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Keywords | Hydrolase/DNA / ba Rossmann-like / DNA repair / TFIIH / nucleus / Hydrolase-DNA complex | ||||||
Function / homology | Function and homology information nucleotide-excision repair factor 3 complex / single-stranded DNA endodeoxyribonuclease activity / Dual incision in TC-NER / DNA endonuclease activity / nucleotide-excision repair / single-stranded DNA binding / transcription by RNA polymerase II / Hydrolases; Acting on ester bonds / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Mietus, M. / Nowak, E. / Jaciuk, M. / Kustosz, P. / Nowotny, M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding. Authors: Mietus, M. / Nowak, E. / Jaciuk, M. / Kustosz, P. / Studnicka, J. / Nowotny, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q10.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q10.ent.gz | 130.2 KB | Display | PDB format |
PDBx/mmJSON format | 4q10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q10_validation.pdf.gz | 460.1 KB | Display | wwPDB validaton report |
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Full document | 4q10_full_validation.pdf.gz | 469.6 KB | Display | |
Data in XML | 4q10_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 4q10_validation.cif.gz | 35.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/4q10 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/4q10 | HTTPS FTP |
-Related structure data
Related structure data | 4q0rSC 4q0wC 4q0zC C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42189.062 Da / Num. of mol.: 2 Fragment: enzyme catalytic core, unp residues 2-111, unp residues 732-986 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RAD2, YGR258C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosseta References: UniProt: P07276, Hydrolases; Acting on ester bonds |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 6945.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide |
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#3: DNA chain | Mass: 7101.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA oligonucleotide |
-Non-polymers , 3 types, 130 molecules
#4: Chemical | #5: Chemical | #6: 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: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 8% (w/v) PEG 8000, 18% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MOPS/HEPES-Na, pH ...Details: 8% (w/v) PEG 8000, 18% (v/v) ethylene glycol, 0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fructose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine, and 0.1 M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.8944 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2013 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8944 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→111.3 Å / Num. all: 29227 / Num. obs: 27918 / % possible obs: 95.52 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4Q0R Resolution: 2.7→43.133 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 32.04 / 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: 2.7→43.133 Å
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Refine LS restraints |
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LS refinement shell |
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