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Yorodumi- PDB-7xt1: Crystal structure of Bypass-of-forespore protein C from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xt1 | ||||||
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Title | Crystal structure of Bypass-of-forespore protein C from Bacillus Subtilis | ||||||
Components | Protein BofC | ||||||
Keywords | SIGNALING PROTEIN / sporulation | ||||||
Function / homology | Bypass of forespore C, C-terminal / Bypass-of-forespore C, N-terminal / Bypass of forespore C, C-terminal domain superfamily / Bypass-of-forespore C, N-terminal domain superfamily / BofC C-terminal domain / Bypass of Forespore C, N terminal / sporulation resulting in formation of a cellular spore / Protein BofC Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.98 Å | ||||||
Authors | Zhang, X.Y. / Jiang, L.G. / Huang, M.D. | ||||||
Funding support | China, 1items
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Citation | Journal: Catalysts / Year: 2022 Title: Structural Studies of Bypass of Forespore Protein C from Bacillus Subtilis to Reveal Its Inhibitory Molecular Mechanism for SpoIVB Authors: Zhang, X. / Sun, G. / Yuan, C. / Jiang, L. / Huang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xt1.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xt1.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 7xt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/7xt1 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/7xt1 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19662.486 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: bofC, BSU27750 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O05391 |
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#2: 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: 1.82 Å3/Da / Density % sol: 32.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium acetate trihydrate pH4.5, 30% w/v polyethylene glycol 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 10268 / % possible obs: 97.9 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.98→2.07 Å / Rmerge(I) obs: 1.421 / Num. unique obs: 988 / CC1/2: 0.693 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.98→46.52 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.665 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 109.76 Å2 / Biso mean: 48.871 Å2 / Biso min: 29.28 Å2
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Refinement step | Cycle: final / Resolution: 1.98→46.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.981→2.032 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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