+Open data
-Basic information
Entry | Database: PDB / ID: 7qv8 | ||||||
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Title | Leishmania infantum BRC1 repeat in complex with LiRAD51 | ||||||
Components |
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Keywords | RECOMBINATION / BRC repeat / homologous recombination / Rad51 / recombinase. BRCA2 | ||||||
Function / homology | Function and homology information mitotic recombination-dependent replication fork processing / DNA strand exchange activity / ATP-dependent activity, acting on DNA / double-strand break repair via homologous recombination / single-stranded DNA binding / double-stranded DNA binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Leishmania infantum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Pantelejevs, T. / Hyvonen, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochem.J. / Year: 2022 Title: Divergent binding mode for a protozoan BRC repeat to RAD51. Authors: Pantelejevs, T. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qv8.cif.gz | 73.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qv8.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qv8_validation.pdf.gz | 864 KB | Display | wwPDB validaton report |
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Full document | 7qv8_full_validation.pdf.gz | 869.5 KB | Display | |
Data in XML | 7qv8_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 7qv8_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/7qv8 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/7qv8 | HTTPS FTP |
-Related structure data
Related structure data | 1n0wS 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: 24838.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: RAD51, LINF_280010500, LINJ_28_0580 / Production host: Escherichia coli (E. coli) / References: UniProt: A4I3C9 |
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#2: Protein/peptide | Mass: 3660.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LINF_200005600, LINJ_20_0070 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4HYJ9 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ADP / |
#5: 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: 1.95 Å3/Da / Density % sol: 36.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 32% low-PEG-smear, 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: LN2 stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→59.61 Å / Num. obs: 12826 / % possible obs: 98.9 % / Redundancy: 23.1 % / Biso Wilson estimate: 57.32 Å2 / CC1/2: 1 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.15→2.18 Å / Redundancy: 18.1 % / Num. unique obs: 632 / CC1/2: 0.5 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1N0W Resolution: 2.15→54.31 Å / SU ML: 0.4145 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.579 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: 74.53 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→54.31 Å
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Refine LS restraints |
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LS refinement shell |
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