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Yorodumi- PDB-8c8s: Crystal structure of human DNA cross-link repair 1A in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 8c8s | ||||||
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Title | Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 21). | ||||||
Components | DNA cross-link repair 1A protein | ||||||
Keywords | HYDROLASE / exonuclease / SNM1A / nuclease inhibition | ||||||
Function / homology | Function and homology information 5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / damaged DNA binding / cell division / nucleoplasm / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Yosaatmadja, Y. / Newman, J.A. / Baddock, H.T. / Bielinski, M. / von Delft, F. / Bountra, C. / McHugh, P.J. / Schofield, C.J. / Gileadi, O. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 21). Authors: Yosaatmadja, Y. / Newman, J.A. / Baddock, H.T. / Bielinski, M. / von Delft, F. / Bountra, C. / McHugh, P.J. / Schofield, C.J. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c8s.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c8s.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 8c8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c8s_validation.pdf.gz | 782.3 KB | Display | wwPDB validaton report |
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Full document | 8c8s_full_validation.pdf.gz | 783.8 KB | Display | |
Data in XML | 8c8s_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8c8s_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/8c8s ftp://data.pdbj.org/pub/pdb/validation_reports/c8/8c8s | HTTPS FTP |
-Related structure data
Related structure data | 8c8bC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38922.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1A, KIAA0086, SNM1, SNM1A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PJP8, beta-lactamase | ||||
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#2: Chemical | ChemComp-U2O / ( | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 30% PEG 1000, 0.1M MIB buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→57.32 Å / Num. obs: 32141 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 28.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 2.785 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1897 / CC1/2: 0.462 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→40.37 Å / SU ML: 0.2562 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9056 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→40.37 Å
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Refine LS restraints |
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LS refinement shell |
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