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Yorodumi- PDB-8c8b: Crystal structure of human DNA cross-link repair 1A in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c8b | ||||||
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Title | Crystal structure of human DNA cross-link repair 1A in complex with hydroxamic acid inhibitor (compound 48). | ||||||
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: 1.46 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: Chem Sci / Year: 2024 Title: Cell-active small molecule inhibitors validate the SNM1A DNA repair nuclease as a cancer target. Authors: Bielinski, M. / Henderson, L.R. / Yosaatmadja, Y. / Swift, L.P. / Baddock, H.T. / Bowen, M.J. / Brem, J. / Jones, P.S. / McElroy, S.P. / Morrison, A. / Speake, M. / van Boeckel, S. / van ...Authors: Bielinski, M. / Henderson, L.R. / Yosaatmadja, Y. / Swift, L.P. / Baddock, H.T. / Bowen, M.J. / Brem, J. / Jones, P.S. / McElroy, S.P. / Morrison, A. / Speake, M. / van Boeckel, S. / van Doornmalen, E. / van Groningen, J. / van den Hurk, H. / Gileadi, O. / Newman, J.A. / McHugh, P.J. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c8b.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c8b.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 8c8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c8b_validation.pdf.gz | 775.3 KB | Display | wwPDB validaton report |
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Full document | 8c8b_full_validation.pdf.gz | 778.2 KB | Display | |
Data in XML | 8c8b_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 8c8b_validation.cif.gz | 24.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/8c8b ftp://data.pdbj.org/pub/pdb/validation_reports/c8/8c8b | HTTPS FTP |
-Related structure data
Related structure data | 8c8dC 8c8sC 8cewC 8cf0C 8cg9C 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-U1L / | ||||
#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 % |
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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: 0.9763 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: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→51.12 Å / Num. obs: 57993 / % possible obs: 98 % / Redundancy: 13.6 % / Biso Wilson estimate: 23.98 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.018 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 1.46→1.5 Å / Rmerge(I) obs: 3.108 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4073 / CC1/2: 0.356 / Rpim(I) all: 0.915 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.46→36.35 Å / SU ML: 0.1909 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7244 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: 35.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→36.35 Å
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Refine LS restraints |
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LS refinement shell |
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