+Open data
-Basic information
Entry | Database: PDB / ID: 4oz5 | ||||||
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Title | Bacillus subtilis HmoB | ||||||
Components | Bacillus subtilis HmoB | ||||||
Keywords | OXIDOREDUCTASE / Heme monooxygenase | ||||||
Function / homology | Function and homology information heme oxygenase (biliverdin-producing) / heme oxygenase (decyclizing) activity / monooxygenase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. spizizenii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å | ||||||
Authors | Choe, J. / Park, S. | ||||||
Citation | Journal: To Be Published Title: Bacillus subtilis HmoB Authors: Choe, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oz5.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oz5.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 4oz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oz5_validation.pdf.gz | 758.2 KB | Display | wwPDB validaton report |
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Full document | 4oz5_full_validation.pdf.gz | 762.6 KB | Display | |
Data in XML | 4oz5_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 4oz5_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/4oz5 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/4oz5 | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17817.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria) Strain: ATCC 6633 / Gene: BSU6633_15062 / Production host: Escherichia coli (E. coli) / References: UniProt: D5N3U6, UniProt: P38049*PLUS |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.3 M Sodium Citrate, 0.5% PEG 2000, 0.1 M HEPES pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 8, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 4635 / % possible obs: 100 % / Redundancy: 25 % / Net I/σ(I): 45.6 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.71→19.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.891 / SU B: 31.988 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.81 Å2
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Refinement step | Cycle: 1 / Resolution: 2.71→19.53 Å
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