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Yorodumi- PDB-4b2p: RadA C-terminal ATPase domain from Pyrococcus furiosus bound to GTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b2p | ||||||
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Title | RadA C-terminal ATPase domain from Pyrococcus furiosus bound to GTP | ||||||
Components | DNA REPAIR AND RECOMBINATION PROTEIN RADA | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information DNA recombinase assembly / mitotic recombination / DNA strand invasion / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / double-stranded DNA binding / single-stranded DNA binding / damaged DNA binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | PYROCOCCUS FURIOSUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Marsh, M.E. / Ehebauer, M.T. / Scott, D. / Abell, C. / Blundell, T.L. / Hyvonen, M. | ||||||
Citation | Journal: FEBS Open Bio / Year: 2016 Title: ATP Half-Sites in Rada and Rad51 Recombinases Bind Nucleotides Authors: Marsh, M.E. / Scott, D.E. / Ehebauer, M.T. / Abell, C. / Blundell, T.L. / Hyvonen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b2p.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b2p.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 4b2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b2p_validation.pdf.gz | 759.9 KB | Display | wwPDB validaton report |
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Full document | 4b2p_full_validation.pdf.gz | 761.1 KB | Display | |
Data in XML | 4b2p_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4b2p_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/4b2p ftp://data.pdbj.org/pub/pdb/validation_reports/b2/4b2p | HTTPS FTP |
-Related structure data
Related structure data | 4a6pC 4a6xC 4d6pC 4uqoC 1pznS S: Starting model for refinement C: citing same article (ref.) |
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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: 25510.150 Da / Num. of mol.: 1 / Fragment: C-TERMINAL ATPASE DOMAIN, RESIDUES 108-349 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS FURIOSUS (archaea) / Plasmid: PBAT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O74036 | ||
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#2: Chemical | ChemComp-GTP / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % / Description: NONE |
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Crystal grow | pH: 6.2 / Details: pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→36.59 Å / Num. obs: 29390 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.79 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.06 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PZN CHAIN A Resolution: 1.6→36.59 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.529 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→36.59 Å
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Refine LS restraints |
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