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Yorodumi- PDB-8cg9: Crystal structure of human DNA cross-link repair 1A in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cg9 | ||||||
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Title | Crystal structure of human DNA cross-link repair 1A in complex with a cyclic N-hydroxyurea inhibitor | ||||||
Components | DNA cross-link repair 1A protein | ||||||
Keywords | HYDROLASE / DNA cross link repair / 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: 1.68 Å | ||||||
Authors | Newman, J.A. / Yosaatmadja, Y. / 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 | 8cg9.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cg9.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cg9_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8cg9_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8cg9_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 8cg9_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/8cg9 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/8cg9 | HTTPS FTP |
-Related structure data
Related structure data | 8c8bC 8c8dC 8c8sC 8cewC 8cf0C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39140.336 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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-Non-polymers , 6 types, 147 molecules
#2: Chemical | ChemComp-NI / |
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#3: Chemical | ChemComp-XOB / Mass: 332.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12N2O5S / Feature type: SUBJECT OF INVESTIGATION |
#4: Chemical | ChemComp-R3Z / |
#5: Chemical | ChemComp-ZN / |
#6: Chemical | ChemComp-SO4 / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / 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: I04 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→57.19 Å / Num. obs: 39243 / % possible obs: 100 % / Redundancy: 25.4 % / Biso Wilson estimate: 26.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.173 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.68→1.72 Å / Rmerge(I) obs: 8.043 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2843 / CC1/2: 0.708 / Rpim(I) all: 1.664 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.68→51.08 Å / SU ML: 0.2195 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.404 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: 40 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→51.08 Å
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Refine LS restraints |
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LS refinement shell |
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