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Yorodumi- PDB-6fw9: Crystal structure of L-tryptophan oxidase VioA from Chromobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fw9 | ||||||
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Title | Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with 6-Fluoro-L-Tryptophan | ||||||
Components | Flavin-dependent L-tryptophan oxidase VioA | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Violacein biosynthesis / L-tryptophan oxidase | ||||||
Function / homology | Function and homology information 7-chloro-L-tryptophan oxidase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Chromobacterium violaceum ATCC 12472 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.739 Å | ||||||
Authors | Lai, H.E. / Morgan, M. / Moore, S. / Freemont, P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biorxiv / Year: 2019 Title: A GenoChemetic strategy for derivatization of the violacein natural product scaffold Authors: Lai, H.E. / Obled, A.M.C. / Chee, S.M. / Morgan, R.M. / Sharma, S.V. / Moore, S.J. / Polizzi, K.M. / Goss, R.J.M. / Freemont, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fw9.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fw9.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 6fw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fw9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6fw9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6fw9_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 6fw9_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/6fw9 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/6fw9 | HTTPS FTP |
-Related structure data
Related structure data | 6fw7C 6fw8C 6fwaC 6ese 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46680.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria) Gene: vioA, CV_3274 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase #2: Chemical | #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: 3.37 Å3/Da / Density % sol: 63.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 9% PEG 8000 and 9% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.739→63.86 Å / Num. obs: 33026 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.97 / Rmerge(I) obs: 0.1456 / Rrim(I) all: 0.1587 / Net I/σ(I): 8.05 |
Reflection shell | Resolution: 2.739→2.828 Å / Redundancy: 6.3 % / Num. unique obs: 3237 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ESE 6ese Resolution: 2.739→63.857 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.5 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.739→63.857 Å
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Refine LS restraints |
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LS refinement shell |
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