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Yorodumi- PDB-3h7j: Crystal structure of BacB, an enzyme involved in Bacilysin synthe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h7j | ||||||
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Title | Crystal structure of BacB, an enzyme involved in Bacilysin synthesis, in monoclinic 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 / MOLECULAR REPLACEMENT / Resolution: 1.87 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 | 3h7j.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h7j.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 3h7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h7j_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 3h7j_full_validation.pdf.gz | 472.1 KB | Display | |
Data in XML | 3h7j_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 3h7j_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/3h7j ftp://data.pdbj.org/pub/pdb/validation_reports/h7/3h7j | HTTPS FTP |
-Related structure data
Related structure data | 3h7ySC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 | #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: 2.27 Å3/Da / Density % sol: 45.71 % |
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Crystal grow | Temperature: 288 K / Method: microbatch / pH: 6.8 Details: 0.1M Tris, 10% PEG 8000, 45% 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: MARRESEARCH / Detector: IMAGE PLATE / Date: May 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→118.68 Å / Num. obs: 39949 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 16.884 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.3 / Num. measured all: 226869 |
Reflection shell | Resolution: 1.865→1.913 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4989 / % possible all: 85.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H7Y Resolution: 1.87→26.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.318 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.145 / ESU R Free: 0.138 / 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: 16.884 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→26.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.865→1.913 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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