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Yorodumi- PDB-5cho: Crystal Structure of BorF, the Flavin Reductase Component of a Ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cho | ||||||
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Title | Crystal Structure of BorF, the Flavin Reductase Component of a Bacterial Two-Component Tryptophan Halogenase | ||||||
Components | Flavin reductase | ||||||
Keywords | HYDROLASE / flavin reductase / two-component halogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||
Authors | Ma, Z. / Bellizzi, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal Structure of BorF, the Flavin Reductase Component of a Bacterial Two-Component Tryptophan Halogenase Authors: Ma, Z. / Bellizzi, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cho.cif.gz | 265.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cho.ent.gz | 213.3 KB | Display | PDB format |
PDBx/mmJSON format | 5cho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cho_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 5cho_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 5cho_validation.xml.gz | 53 KB | Display | |
Data in CIF | 5cho_validation.cif.gz | 65.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/5cho ftp://data.pdbj.org/pub/pdb/validation_reports/ch/5cho | HTTPS FTP |
-Related structure data
Related structure data | 4hx6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21153.658 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: borF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: M9QXS1 #2: Chemical | ChemComp-FAD / #3: 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: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: Drop containing 1 uL of 10 mg/mL (0.474 mM) BorF in 20 mM Tris pH 7.5, 100 mM NaCl, with 1 mM FAD mixed with 1 uL of reservoir solution containing 20% PEG 400, 0.1 M HEPES pH 7.6, 5% v/v ...Details: Drop containing 1 uL of 10 mg/mL (0.474 mM) BorF in 20 mM Tris pH 7.5, 100 mM NaCl, with 1 mM FAD mixed with 1 uL of reservoir solution containing 20% PEG 400, 0.1 M HEPES pH 7.6, 5% v/v glycerol against 200 micro liter reservoir PH range: 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.988 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→50.937 Å / Num. obs: 64289 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.37→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HX6 Resolution: 2.37→47.607 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.8 Å2 / Biso mean: 53.2596 Å2 / Biso min: 16.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.37→47.607 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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