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- PDB-7cd4: Crystal structure of the S103F mutant of Bacillus subtilis (natto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cd4 | ||||||
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Title | Crystal structure of the S103F mutant of Bacillus subtilis (natto) YabJ protein. | ||||||
![]() | YabJ protein | ||||||
![]() | UNKNOWN FUNCTION / Mutant / Homotetramer | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujimoto, Z. / Kishine, N. / Kimura, K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.4 KB | Display | ![]() |
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Full document | ![]() | 465 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5y6uSC ![]() 7cd2C ![]() 7cd3C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 13727.664 Da / Num. of mol.: 4 / Mutation: S103F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BEST195 / Gene: yabJ, BSNT_00084 / Plasmid: pET22b(+) / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 209 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-BTB / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 13.5 % PEG 3350, 1 mM zinc acetate, 0.2 M magnesium chloride, 0.1 M Bis-Tris buffer pH 5.5 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. obs: 34597 / % possible obs: 99.3 % / Redundancy: 13.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.109 / Χ2: 1.037 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3 / Num. unique obs: 3375 / Χ2: 1.184 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5Y6U Resolution: 2.1→66.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.593 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.164 / 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: 34.553 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→66.68 Å
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Refine LS restraints |
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