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Yorodumi- PDB-6vmf: Crystal structure of the Y766F mutant of GoxA soaked with glycine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vmf | ||||||
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Title | Crystal structure of the Y766F mutant of GoxA soaked with glycine | ||||||
Components | Glycine oxidase | ||||||
Keywords | OXIDOREDUCTASE / CTQ | ||||||
Function / homology | L-Lysine epsilon oxidase, N-terminal / L-lysine epsilon oxidase, C-terminal / L-Lysine epsilon oxidase N-terminal / L-lysine epsilon oxidase C-terminal domain / metal ion binding / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudoalteromonas luteoviolacea DSM 6061 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.24 Å | ||||||
Authors | Yukl, E.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Roles of active-site residues in catalysis, substrate binding, cooperativity, and the reaction mechanism of the quinoprotein glycine oxidase. Authors: Mamounis, K.J. / Yukl, E.T. / Davidson, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vmf.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6vmf.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6vmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vmf_validation.pdf.gz | 491.8 KB | Display | wwPDB validaton report |
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Full document | 6vmf_full_validation.pdf.gz | 547.6 KB | Display | |
Data in XML | 6vmf_validation.xml.gz | 116.8 KB | Display | |
Data in CIF | 6vmf_validation.cif.gz | 162.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/6vmf ftp://data.pdbj.org/pub/pdb/validation_reports/vm/6vmf | HTTPS FTP |
-Related structure data
Related structure data | 6vl7C 6vmvC 6vmwC 6bywS 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: 91569.852 Da / Num. of mol.: 4 / Mutation: Y766F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas luteoviolacea DSM 6061 (bacteria) Gene: N475_19905 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A161XU12 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.5 Details: Protein at 10 mg/mL was combined in a 1:1 ratio with precipitant solution composed of 23% PEG 3350, 0.1 M HEPES pH 7.5, 0.1 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2018 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→48.421 Å / Num. obs: 173760 / % possible obs: 98 % / Redundancy: 3.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.074 / Rrim(I) all: 0.143 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.24→2.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8718 / CC1/2: 0.685 / Rpim(I) all: 0.384 / Rrim(I) all: 0.75 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6BYW Resolution: 2.24→48.421 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.39 Å2 / Biso mean: 51.8777 Å2 / Biso min: 11.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.24→48.421 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 14.8958 Å / Origin y: -142.8242 Å / Origin z: 231.3668 Å
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Refinement TLS group |
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