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Open data
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Basic information
Entry | Database: PDB / ID: 7w43 | ||||||
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Title | Crystal structure of Bacillus subtilis YjoB N-terminal domain | ||||||
![]() | 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 | ![]() | 377.4 KB | Display | ![]() |
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PDB format | ![]() | 313.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515 KB | Display | ![]() |
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Full document | ![]() | 533 KB | Display | |
Data in XML | ![]() | 61 KB | Display | |
Data in CIF | ![]() | 81.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w42SC ![]() 7w46C 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: 19002.100 Da / Num. of mol.: 12 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: yjoB, BSU12420 / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.24 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 8.5 Details: 30% (w/v) isopropanol, 0.1 M Tris-HCl, 30% (w/v) PEG 3350 |
-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 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 39002 / % possible obs: 96.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1935 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7W42 Resolution: 3→49.36 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.7 / 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: 148.09 Å2 / Biso mean: 83.5247 Å2 / Biso min: 40.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→49.36 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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