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Open data
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Basic information
Entry | Database: PDB / ID: 7w42 | ||||||
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Title | Crystal structure of Bacillus subtilis YjoB | ||||||
![]() | Uncharacterized ATPase YjoB | ||||||
![]() | HYDROLASE / AAA protein / chaperone | ||||||
Function / homology | ![]() protein import into peroxisome matrix / Hydrolases / peroxisomal membrane / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dahal, P. / Kwon, E. / Kim, D.Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure and biochemical analysis suggest that YjoB ATPase is a putative substrate-specific molecular chaperone. Authors: Kwon, E. / Dahal, P. / Kim, D.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.5 KB | Display | ![]() |
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PDB format | ![]() | 139.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w43C ![]() 7w46C 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48975.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: yjoB, BSU12420 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.13 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 5% (v/v) PEG 400, 2 M ammonium, citrate/citric acid (pH 7.5), 10 mM TCEP |
-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: Sep 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.619→50 Å / Num. obs: 42649 / % possible obs: 99.8 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.62→2.72 Å / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4419 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 114.03 Å2 / Biso mean: 49.2697 Å2 / Biso min: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.619→36.302 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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