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Open data
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Basic information
Entry | Database: PDB / ID: 6tvv | ||||||
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Title | Crystal structure of 3'-5' RecJ exonuclease from M. Jannaschii | ||||||
![]() | MjaRecJ | ||||||
![]() | DNA BINDING PROTEIN / RecJ / exonuclease / DNA recombination and repair / archaea / resolution | ||||||
Function / homology | DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / nucleic acid binding / : / Uncharacterized protein MJ0831![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | De March, M. / Medagli, B. / Krastanova, I. / Saha, I. / Pisani, F. / Onesti, S. | ||||||
![]() | ![]() Title: Crystal structure of 3'-5' RecJ exonuclease from M. Jannaschii Authors: De March, M. / Medagli, B. / Krastanova, I. / Saha, I. / Pisani, F. / Onesti, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.9 KB | Display | ![]() |
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PDB format | ![]() | 134.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 0 - 426 / Label seq-ID: 1 - 427
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Components
#1: Protein | Mass: 48905.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MJ0831 / Production host: ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium citrate, 0.1 M Bis-Tris-Propane pH 8.5, 14-24 % w/v PEG 3350, 10 mM MnCl2 |
-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: Jun 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.89113 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→99.9 Å / Num. obs: 30267 / % possible obs: 99.2 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.8→2.95 Å / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4308 / CC1/2: 0.378 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 51.281 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→87.33 Å
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Refine LS restraints |
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