+Open data
-Basic information
Entry | Database: PDB / ID: 5mbs | ||||||
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Title | Crystal structure of Bacillus subtilis EngA in space group P21 | ||||||
Components | GTPase Der | ||||||
Keywords | HYDROLASE / GTPase / EngA | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | da Silveira Tome, C. / Foucher, A.E. / Jault, J.M. / Housset, D. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Bacillus subtilis EngA in space group P21 Authors: da Silveira Tome, C. / Foucher, A.E. / Jault, J.M. / Housset, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mbs.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mbs.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mbs_validation.pdf.gz | 704.7 KB | Display | wwPDB validaton report |
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Full document | 5mbs_full_validation.pdf.gz | 707 KB | Display | |
Data in XML | 5mbs_validation.xml.gz | 16 KB | Display | |
Data in CIF | 5mbs_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/5mbs ftp://data.pdbj.org/pub/pdb/validation_reports/mb/5mbs | HTTPS FTP |
-Related structure data
Related structure data | 4dcuS S: Starting model for refinement |
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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: 48828.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: der, B4122_2158, B4417_1159 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A164XD11, UniProt: P50743*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GDP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.5 M sodium sulfate 0.1 M Tris pH 6.5 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→61.62 Å / Num. obs: 6572 / % possible obs: 98.5 % / Redundancy: 3.27 % / Biso Wilson estimate: 88.6 Å2 / CC1/2: 0.996 / Rsym value: 0.093 / Net I/σ(I): 9.69 |
Reflection shell | Resolution: 3.2→3.28 Å / Redundancy: 3.21 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.67 / CC1/2: 0.497 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DCU Resolution: 3.2→61.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.775 / Cross valid method: THROUGHOUT / ESU R Free: 0.917 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.206 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→61.62 Å
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