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Yorodumi- PDB-4jh3: Crystal Structure of FosB from Bacillus cereus with Zinc and Fosf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jh3 | ||||||
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Title | Crystal Structure of FosB from Bacillus cereus with Zinc and Fosfomycin | ||||||
Components | Metallothiol transferase FosB | ||||||
Keywords | TRANSFERASE / Bacillithiol-S-Transferase | ||||||
Function / homology | Function and homology information Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity, transferring alkyl or aryl (other than methyl) groups / response to antibiotic / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Thompson, M.K. / Harp, J. / Keithly, M.E. / Jagessar, K. / Cook, P.D. / Armstrong, R.N. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural and Chemical Aspects of Resistance to the Antibiotic Fosfomycin Conferred by FosB from Bacillus cereus. Authors: Thompson, M.K. / Keithly, M.E. / Harp, J. / Cook, P.D. / Jagessar, K.L. / Sulikowski, G.A. / Armstrong, R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jh3.cif.gz | 145.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jh3.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 4jh3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jh3 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jh3 | HTTPS FTP |
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-Related structure data
Related structure data | 4jh1C 4jh2C 4jh4C 4jh5C 4jh6C 4jh7C 4jh8C 4jh9C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 16488.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: fosB, BCE_2111 / Production host: Escherichia coli (E. coli) References: UniProt: Q739M9, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
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-Non-polymers , 6 types, 326 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, Magnesium formate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.28 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 19, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→30 Å / Num. obs: 49820 / % possible obs: 98.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.095 / Χ2: 0.986 / Net I/σ(I): 9.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1633 / WRfactor Rwork: 0.1217 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9179 / SU B: 1.959 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0685 / SU Rfree: 0.0635 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 87.64 Å2 / Biso mean: 17.7578 Å2 / Biso min: 6.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.495→1.534 Å / Total num. of bins used: 20
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