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- PDB-4b2p: RadA C-terminal ATPase domain from Pyrococcus furiosus bound to GTP -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b2p | ||||||
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Title | RadA C-terminal ATPase domain from Pyrococcus furiosus bound to GTP | ||||||
![]() | DNA REPAIR AND RECOMBINATION PROTEIN RADA | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() DNA recombinase assembly / mitotic recombination / DNA strand invasion / DNA strand exchange activity / ATP-dependent DNA damage sensor activity / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Marsh, M.E. / Ehebauer, M.T. / Scott, D. / Abell, C. / Blundell, T.L. / Hyvonen, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.7 KB | Display | ![]() |
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PDB format | ![]() | 42.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.9 KB | Display | ![]() |
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Full document | ![]() | 761.1 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a6pC ![]() 4a6xC ![]() 4d6pC ![]() 4uqoC ![]() 1pznS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-GTP / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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