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Open data
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Basic information
Entry | Database: PDB / ID: 7yos | ||||||||||||
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Title | Recj2 and Mn complex from Methanocaldococcus jannaschii | ||||||||||||
![]() | nuclease RecJ2 | ||||||||||||
![]() | DNA BINDING PROTEIN / Recj2 / Mn / complex / Methanocaldococcus jannaschii | ||||||||||||
Function / homology | DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / nucleic acid binding / : / Uncharacterized protein MJ0831![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wang, W.W. / Liu, X.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of nuclease RecJ2 from Methanocaldococcus jannaschii Authors: Wang, W.W. / Yi, G.S. / Zhou, H. / Zhao, Y.X. / Wang, Q.S. / He, J.H. / Yu, F. / Xiao, X. / Liu, X.P. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179 KB | Display | ![]() |
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PDB format | ![]() | 141.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 42.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yoqC ![]() 7yorC ![]() 7yikS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 48905.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MJ0831 / Production host: ![]() ![]() #2: Chemical | #3: 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: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 400, 50mM HEPES pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.17→175.82 Å / Num. obs: 98625 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 34.87 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.044 / Rrim(I) all: 0.098 / Net I/σ(I): 12.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7YIK Resolution: 2.17→48.047 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.25 / Stereochemistry target values: ML
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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 max: 105.5 Å2 / Biso mean: 43.3946 Å2 / Biso min: 15.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.17→48.047 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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