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Yorodumi- PDB-6gz8: First GerMN domain of the sporulation protein GerM from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gz8 | |||||||||
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Title | First GerMN domain of the sporulation protein GerM from Bacillus subtilis | |||||||||
Components | Spore germination protein GerMGermination | |||||||||
Keywords | STRUCTURAL PROTEIN / GerM / GerMN domain / lipoprotein / sporulation / endospores / secretion systems | |||||||||
Function / homology | GerMN domain / Sporulation and spore germination / Sporulation and spore germination / sporulation resulting in formation of a cellular spore / Prokaryotic membrane lipoprotein lipid attachment site profile. / Spore germination protein GerM Function and homology information | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å | |||||||||
Authors | Trouve, J. / Mohamed, A. / Leisico, F. / Contreras-Martel, C. / Liu, B. / Mas, C. / Rudner, D.Z. / Rodrigues, C.D.A. / Morlot, C. | |||||||||
Funding support | France, Australia, 2items
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Citation | Journal: J. Struct. Biol. / Year: 2018 Title: Structural characterization of the sporulation protein GerM from Bacillus subtilis. Authors: Trouve, J. / Mohamed, A. / Leisico, F. / Contreras-Martel, C. / Liu, B. / Mas, C. / Rudner, D.Z. / Rodrigues, C.D.A. / Morlot, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gz8.cif.gz | 122.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gz8.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/6gz8 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/6gz8 | HTTPS FTP |
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-Related 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: 15328.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 Gene: gerM, BSU28380 / Plasmid: pCR282 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P39072 | ||||
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#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-EDO / | #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: 2.18 Å3/Da / Density % sol: 43.52 % / Description: large 3D needles |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M sodium acetate 21% PEG 3350 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. obs: 68958 / % possible obs: 94.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.46 Å2 / Rrim(I) all: 0.07 / Rsym value: 0.061 / Net I/σ(I): 11.22 |
Reflection shell | Resolution: 1→1.06 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.95 / Num. unique obs: 10428 / Rrim(I) all: 0.42 / Rsym value: 0.356 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1→41.32 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.806 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.021 / ESU R Free: 0.022 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.292 Å2
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Refinement step | Cycle: 1 / Resolution: 1→41.32 Å
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Refine LS restraints |
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