[English] 日本語
Yorodumi- PDB-4dcs: Crystal Structure of B. subtilis EngA in complex with sulfate ion... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dcs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of B. subtilis EngA in complex with sulfate ion and GDP | ||||||
Components | GTP-BINDING PROTEIN ENGA | ||||||
Keywords | HYDROLASE / GTPASE / ENGA / GDP / PROTEIN BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Reiser, J.-B. / Housset, D. / Foucher, A.-E. / Jault, J.-M. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Potassium Acts as a GTPase-Activating Element on Each Nucleotide-Binding Domain of the Essential Bacillus subtilis EngA. Authors: Foucher, A.E. / Reiser, J.B. / Ebel, C. / Housset, D. / Jault, J.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dcs.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dcs.ent.gz | 73 KB | Display | PDB format |
PDBx/mmJSON format | 4dcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dcs_validation.pdf.gz | 793.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4dcs_full_validation.pdf.gz | 799.3 KB | Display | |
Data in XML | 4dcs_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 4dcs_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dcs ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dcs | HTTPS FTP |
-Related structure data
Related structure data | 4dctC 4dcuC 4dcvC 2hjgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50999.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: der, engA, yphC, BSU22840 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P50743 |
---|---|
#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 4% to 10% PEG 3350 v/w, 100 mM Mes, 300 mM amonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.282 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2009 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.282 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. all: 22133 / Num. obs: 22133 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.25→2.35 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 5 / Num. unique all: 2523 / Rsym value: 0.406 / % possible all: 92.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HJG Resolution: 2.25→19.93 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 6.658 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.352 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.603 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→19.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
|