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Yorodumi- PDB-7cd2: Crystal structure of the S103F mutant of Bacillus subtilis (natto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cd2 | ||||||
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Title | Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein. | ||||||
Components | YabJ protein | ||||||
Keywords | UNKNOWN FUNCTION / Mutant / Homotetramer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. natto (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Fujimoto, Z. / Kishine, N. / Kimura, K. | ||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2021 Title: Tetramer formation of Bacillus subtilis YabJ protein that belongs to YjgF/YER057c/UK114 family. Authors: Fujimoto, Z. / Hong, L.T.T. / Kishine, N. / Suzuki, N. / Kimura, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cd2.cif.gz | 415.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cd2.ent.gz | 342.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cd2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cd2_validation.pdf.gz | 568.5 KB | Display | wwPDB validaton report |
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Full document | 7cd2_full_validation.pdf.gz | 595.7 KB | Display | |
Data in XML | 7cd2_validation.xml.gz | 66.8 KB | Display | |
Data in CIF | 7cd2_validation.cif.gz | 96 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/7cd2 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/7cd2 | HTTPS FTP |
-Related structure data
Related structure data | 5y6uSC 7cd3C 7cd4C 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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Unit cell |
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-Components
#1: Protein | Mass: 13727.664 Da / Num. of mol.: 20 / Mutation: S103F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. natto (strain BEST195) (bacteria) Strain: BEST195 / Gene: yabJ, BSNT_00084 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D4G3D4 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 25% PEG 4000, 0.45 M ammonium acetate, 0.1 M sodium acetate buffer pH 4.2 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→150 Å / Num. obs: 62923 / % possible obs: 93.3 % / Redundancy: 11.8 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.207 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.733 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 6046 / Χ2: 1.397 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y6U Resolution: 2.7→39.912 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.892 / SU B: 16.258 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / 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: 54.087 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→39.912 Å
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