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Yorodumi- PDB-4dct: Crystal Structure of B. subtilis EngA in complex with half-occupa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dct | ||||||
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Title | Crystal Structure of B. subtilis EngA in complex with half-occupacy 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: 2.3 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dct.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dct.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 4dct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dct ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dct | HTTPS FTP |
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-Related structure data
Related structure data | 4dcsC 4dcuC 4dcvC 2hjgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG 3350 w/v, 100 mM Mes, 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2010 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42 Å / Num. all: 20375 / Num. obs: 20375 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2300 / Rsym value: 0.486 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2HJG Resolution: 2.3→41.97 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.87 / SU B: 9.01 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.439 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 43.864 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→41.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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