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- PDB-8dtd: Crystal Structure of FosB from Bacillus cereus with Zinc and Phos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dtd | ||||||
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Title | Crystal Structure of FosB from Bacillus cereus with Zinc and Phosphonoformate | ||||||
![]() | Metallothiol transferase FosB | ||||||
![]() | TRANSFERASE / fosfomycin / antibiotic resistance / thiol-transferase / ANTIBIOTIC / dimer / TRANSFERASE-ANTIBIOTIC complex | ||||||
Function / homology | ![]() transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / response to antibiotic / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Travis, S. / Gilbert, N.C. / Thompson, M.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition of FosB by PPF Authors: Travis, S. / Thompson, M.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 | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jh3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16488.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, Magnesium formate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→83.75 Å / Num. obs: 29716 / % possible obs: 99.6 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.036 / Rrim(I) all: 0.131 / Net I/σ(I): 14.2 / Num. measured all: 387161 / Scaling rejects: 24 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JH3 Resolution: 1.95→51.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.396 / SU ML: 0.142 / SU R Cruickshank DPI: 0.1661 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.154 / 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: 92.2 Å2 / Biso mean: 35.549 Å2 / Biso min: 20.43 Å2
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Refinement step | Cycle: final / Resolution: 1.95→51.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.952→2.003 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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