[English] 日本語
Yorodumi- PDB-7bkf: Crystal structure of WT BA3943, a CE4 family pseudoenzyme from Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bkf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of WT BA3943, a CE4 family pseudoenzyme from Bacillus Anthracis | ||||||
Components | Putative polysaccharide deacetylase | ||||||
Keywords | UNKNOWN FUNCTION / Polysaccharide / Deacetylase / Peptidoglycan / Pseudoenzyme / Sporulation. | ||||||
Function / homology | Sporulation protein, polysaccharide deacetylase, YlxY / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Glycoside hydrolase/deacetylase, beta/alpha-barrel / carbohydrate metabolic process / Putative polysaccharide deacetylase Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.139 Å | ||||||
Authors | Molfetas, A. / Kokkinidis, M. | ||||||
Funding support | Greece, 1items
| ||||||
Citation | Journal: To Be Published Title: The resurrection of a dead enzyme Authors: Molfetas, A. / Tomatsidou, N. / Bouriotis, V. / Kokkinidis, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bkf.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bkf.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 7bkf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/7bkf ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bkf | HTTPS FTP |
---|
-Related structure data
Related structure data | 6hpaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32910.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: ylxY, BA_3943, A9486_19545, BASH2_01993, COL95_11150 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6H3AKM9 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: (NH4)2SO4 CH3COONA PH=5 / PH range: 5.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 6, 2017 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.139→40.7 Å / Num. obs: 92525 / % possible obs: 96.1 % / Redundancy: 6.0872 % / Biso Wilson estimate: 19.3 Å2 / Rrim(I) all: 0.075 / Net I/σ(I): 11.14 |
Reflection shell | Resolution: 1.14→1.21 Å / Mean I/σ(I) obs: 0.33 / Num. unique obs: 12163 / CC1/2: 0.16 / % possible all: 79 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HPA Resolution: 1.139→40.656 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 27.37 / 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: 77.78 Å2 / Biso mean: 24.2257 Å2 / Biso min: 12.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.139→40.656 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|