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Yorodumi- PDB-3h7y: Crystal structure of BacB, an enzyme involved in Bacilysin synthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h7y | ||||||
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Title | Crystal structure of BacB, an enzyme involved in Bacilysin synthesis, in tetragonal form | ||||||
Components | Bacilysin biosynthesis protein bacB | ||||||
Keywords | BIOSYNTHETIC PROTEIN / BacB / YwfC / Bacilysin synthesis / Anticapsin synthesis / Bi-cupin / Double stranded beta helix / Antibiotic biosynthesis | ||||||
Function / homology | Function and homology information 3-[(4R)-4-hydroxycyclohexa-1,5-dien-1-yl]-2-oxopropanoate isomerase / intramolecular oxidoreductase activity, transposing C=C bonds / cobalt ion binding / antibiotic biosynthetic process / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.22 Å | ||||||
Authors | Rajavel, M. / Gopal, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Role of Bacillus subtilis BacB in the synthesis of bacilysin Authors: Rajavel, M. / Mitra, A. / Gopal, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h7y.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h7y.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 3h7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h7y ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h7y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | BACB IS MONOMER IN SOLUTION, BUT DIMER IN CRYSTAL STRUCTURE |
-Components
#1: Protein | Mass: 27946.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ywfC, bacB / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P39639 #2: Chemical | ChemComp-CO / #3: Chemical | #4: Chemical | ChemComp-FE / | #5: 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: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 288 K / Method: microbatch / pH: 6.8 Details: 0.1M Tris, 10% PEG 8000, 60% MPD, 0.2M NaCl, pH 6.8, Micro batch, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→35.25 Å / Num. obs: 25906 / % possible obs: 99.58 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 22.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 31.3 / Num. measured all: 573250 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 23.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 10.1 / Num. unique all: 3264 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.22→34.33 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.882 / SU B: 11.711 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.285 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.037 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→34.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.221→2.279 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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