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Yorodumi- PDB-6fwa: Crystal structure of L-tryptophan oxidase VioA from Chromobacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fwa | |||||||||
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Title | Crystal structure of L-tryptophan oxidase VioA from Chromobacterium violaceum in complex with 7-Methyl-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 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.846 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 | 6fwa.cif.gz | 180 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fwa.ent.gz | 139.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/6fwa ftp://data.pdbj.org/pub/pdb/validation_reports/fw/6fwa | HTTPS FTP |
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-Related structure data
Related structure data | 6fw7C 6fw8C 6fw9C 6esdS 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 (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (bacteria) Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 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: 3.29 Å3/Da / Density % sol: 62.65 % |
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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: 2.846→47.134 Å / Num. obs: 29251 / % possible obs: 95 % / Redundancy: 6.5 % / CC1/2: 0.975 / Rmerge(I) obs: 0.1922 / Rrim(I) all: 0.2095 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.846→2.947 Å / Redundancy: 6.4 % / Num. unique obs: 2837 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ESD Resolution: 2.846→47.134 Å / SU ML: 0.49 / σ(F): 1.33 / Phase error: 36.26 / 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: 2.846→47.134 Å
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Refine LS restraints |
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LS refinement shell |
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