+Open data
-Basic information
Entry | Database: PDB / ID: 7w46 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Bacillus subtilis YjoB with ADP | ||||||
Components | Uncharacterized ATPase YjoB | ||||||
Keywords | HYDROLASE / AAA protein / chaperone | ||||||
Function / homology | Function and homology information protein import into peroxisome matrix / Hydrolases / peroxisomal membrane / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Dahal, P. / Kwon, E. / Kim, D.Y. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7w46.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7w46.ent.gz | 138.5 KB | Display | PDB format |
PDBx/mmJSON format | 7w46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w46_validation.pdf.gz | 799.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7w46_full_validation.pdf.gz | 808.5 KB | Display | |
Data in XML | 7w46_validation.xml.gz | 30.9 KB | Display | |
Data in CIF | 7w46_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/7w46 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/7w46 | HTTPS FTP |
-Related structure data
Related structure data | 7w42SC 7w43C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 48975.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: yjoB, BSU12420 / Production host: Escherichia coli B (bacteria) / References: UniProt: O34703, Hydrolases #2: Chemical | ChemComp-ADP / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 7.5 Details: 5% (v/v) PEG 400, 2 M ammonium citrate/citric acid, 10 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9793 Å |
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: 2.7→50 Å / Num. obs: 39371 / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.7→2.81 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4361 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7W42 Resolution: 2.7→45.122 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.16 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.5 Å2 / Biso mean: 49.7228 Å2 / Biso min: 19.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→45.122 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|