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Yorodumi- PDB-5zbc: Crystal structure of Se-Met tryptophan oxidase (C395A mutant) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zbc | ||||||
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Title | Crystal structure of Se-Met tryptophan oxidase (C395A mutant) from Chromobacterium violaceum | ||||||
Components | Flavin-dependent L-tryptophan oxidase VioA | ||||||
Keywords | OXIDOREDUCTASE / Oxidase | ||||||
Function / homology | 7-chloro-L-tryptophan oxidase / Amine oxidase / Flavin containing amine oxidoreductase / antibiotic biosynthetic process / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / metal ion binding / FLAVIN-ADENINE DINUCLEOTIDE / Flavin-dependent L-tryptophan oxidase VioA Function and homology information | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Yamaguchi, H. / Tatsumi, M. / Takahashi, K. / Tagami, U. / Sugiki, M. / Kashiwagi, T. / Okazaki, S. / Mizukoshi, T. / Asano, Y. | ||||||
Citation | Journal: J. Biochem. / Year: 2018 Title: Protein engineering for improving the thermostability of tryptophan oxidase and insights from structural analysis. Authors: Yamaguchi, H. / Tatsumi, M. / Takahashi, K. / Tagami, U. / Sugiki, M. / Kashiwagi, T. / Kameya, M. / Okazaki, S. / Mizukoshi, T. / Asano, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zbc.cif.gz | 179.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zbc.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zbc_validation.pdf.gz | 941.5 KB | Display | wwPDB validaton report |
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Full document | 5zbc_full_validation.pdf.gz | 946.2 KB | Display | |
Data in XML | 5zbc_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 5zbc_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/5zbc ftp://data.pdbj.org/pub/pdb/validation_reports/zb/5zbc | HTTPS FTP |
-Related 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: 51040.914 Da / Num. of mol.: 2 / Mutation: C395A 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 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9S3V1, 7-chloro-L-tryptophan oxidase #2: Chemical | #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: 2.37 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.1M MES, 40% Polyethylene glycol 400, pH6.8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9789 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 6, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→70.07 Å / Num. obs: 45946 / % possible obs: 100 % / Redundancy: 14.595 % / Biso Wilson estimate: 38.053 Å2 / Rmerge F obs: 0.042 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.079 / Net I/σ(I): 21.09 / Num. measured all: 670570 / Scaling rejects: 804 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.2→70.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2361 / WRfactor Rwork: 0.1784 / FOM work R set: 0.863 / SU B: 5.099 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2495 / SU Rfree: 0.2007 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 150.02 Å2 / Biso mean: 34.804 Å2 / Biso min: 15.38 Å2
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Refinement step | Cycle: final / Resolution: 2.2→70.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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