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- PDB-8cew: Crystal structure of human DNA cross-link repair 1A in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cew | ||||||
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Title | Crystal structure of human DNA cross-link repair 1A in complex with N-hydroxyimide inhibitor H1 | ||||||
![]() | DNA cross-link repair 1A protein | ||||||
![]() | HYDROLASE / SNM1A / nuclease inhibition / ICL | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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 | ![]()
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![]() | ![]() Title: Crystal structure of human DNA cross-link repair 1A in complex with N-hydroxyimide inhibitor H1 Authors: Newman, J.A. / Yosaatmadja, Y. / 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.4 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 260 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DMS / | ||
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#3: Chemical | ChemComp-NI / | ||
#4: Chemical | ChemComp-ZN / | ||
#5: Chemical | Mass: 243.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9NO4 / Feature type: SUBJECT OF INVESTIGATION #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.02 % |
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Crystal grow | Temperature: 278 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→36.13 Å / Num. obs: 51062 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 23.19 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.53→1.57 Å / Rmerge(I) obs: 0.985 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3716 / CC1/2: 0.609 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 31.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→36.13 Å
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Refine LS restraints |
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LS refinement shell |
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