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Yorodumi- PDB-4jh8: Crystal Structure of FosB from Bacillus cereus with Zinc and L-Cy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jh8 | ||||||
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Title | Crystal Structure of FosB from Bacillus cereus with Zinc and L-Cysteine-Fosfomycin Ternary Complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.41 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 | 4jh8.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jh8.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 4jh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jh8 ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jh8 | HTTPS FTP |
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-Related structure data
Related structure data | 4jh1C 4jh2C 4jh3C 4jh4C 4jh5C 4jh6C 4jh7C 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, 261 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Chemical | ChemComp-CYS / #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: 47.3 % |
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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: 1.078 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 7, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.41→50 Å / Num. obs: 59747 / % possible obs: 99.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.048 / Χ2: 1.202 / Net I/σ(I): 11.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→48.92 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1811 / WRfactor Rwork: 0.1432 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9202 / SU B: 1.646 / SU ML: 0.03 / SU R Cruickshank DPI: 0.058 / SU Rfree: 0.0552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.055 / 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: 94 Å2 / Biso mean: 19.7407 Å2 / Biso min: 7.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.41→48.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.409→1.446 Å / Total num. of bins used: 20
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