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Yorodumi- PDB-5q4v: PanDDA analysis group deposition -- Crystal Structure of DCLRE1A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5q4v | ||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of DCLRE1A after initial refinement with no ligand modelled (structure 96) | ||||||
Components | DCLRE1A | ||||||
Keywords | HYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
Function / homology | Function and homology information 5'-3' DNA exonuclease activity / interstrand cross-link repair / Fanconi Anemia Pathway / fibrillar center / double-strand break repair via nonhomologous end joining / beta-lactamase activity / 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 / molecular replacement / Resolution: 1.59 Å | ||||||
Authors | Newman, J.A. / Aitkenhead, H. / Lee, S.Y. / Kupinska, K. / Burgess-Brown, N. / Tallon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Newman, J.A. / Aitkenhead, H. / Lee, S.Y. / Kupinska, K. / Burgess-Brown, N. / Tallon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Citation | Journal: To Be Published Title: PanDDA analysis group deposition Authors: Newman, J.A. / Aitkenhead, H. / Lee, S.Y. / Kupinska, K. / Burgess-Brown, N. / Tallon, R. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5q4v.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5q4v.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 5q4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5q4v_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 5q4v_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 5q4v_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5q4v_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/5q4v ftp://data.pdbj.org/pub/pdb/validation_reports/q4/5q4v | HTTPS FTP |
-Group deposition
ID | G_1002036 (281 entries) |
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Title | PanDDA analysis group deposition |
Type | undefined |
Description | Nuclease domain of human DCLRE1A screened against the DSPL Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 5ahoS 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
#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 |
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#2: Chemical | ChemComp-MLI / |
#3: Chemical | ChemComp-NI / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | smiles string of soaked compound: CCc1ccccc1NNC(=S)N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.46 % / Mosaicity: 0 ° |
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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 source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||||||||
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Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.59→57.26 Å / Num. obs: 47347 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Rrim(I) all: 0.094 / Net I/σ(I): 12.2 / Num. measured all: 307154 / Scaling rejects: 0 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5aho Resolution: 1.59→57.26 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.518 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 216.88 Å2 / Biso mean: 41.449 Å2 / Biso min: 12.29 Å2
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Refinement step | Cycle: final / Resolution: 1.59→57.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.631 Å / Total num. of bins used: 20
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