+Open data
-Basic information
Entry | Database: PDB / ID: 6ubr | ||||||
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Title | Crystal structure of D678A GoxA bound to glycine at pH 7.5 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | OXIDOREDUCTASE / tryotiophylquinone / oxidase | ||||||
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 / GLYCINE / DI(HYDROXYETHYL)ETHER / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudoalteromonas luteoviolacea DSM 6061 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Yukl, E.T. / Avalos, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Kinetic and structural evidence that Asp-678 plays multiple roles in catalysis by the quinoprotein glycine oxidase. Authors: Mamounis, K.J. / Avalos, D. / 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 | 6ubr.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ubr.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6ubr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ubr_validation.pdf.gz | 512.6 KB | Display | wwPDB validaton report |
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Full document | 6ubr_full_validation.pdf.gz | 567.6 KB | Display | |
Data in XML | 6ubr_validation.xml.gz | 128.6 KB | Display | |
Data in CIF | 6ubr_validation.cif.gz | 187.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/6ubr ftp://data.pdbj.org/pub/pdb/validation_reports/ub/6ubr | HTTPS FTP |
-Related structure data
Related structure data | 6ubnC 6ubzC 6uc1C 6ufqC 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
-Protein , 1 types, 4 molecules BACD
#1: Protein | Mass: 91482.781 Da / Num. of mol.: 4 / Mutation: D678A 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 |
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-Non-polymers , 5 types, 2176 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-GLY / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.76 Å3/Da / Density % sol: 55.46 % |
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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 a solution containing 21% PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES pH 7.5 |
-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: Jun 30, 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: 1.96→48.29 Å / Num. obs: 271688 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.042 / Rrim(I) all: 0.081 / Net I/σ(I): 11.5 / Num. measured all: 951567 / Scaling rejects: 402 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BYW Resolution: 1.96→48.288 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 196.81 Å2 / Biso mean: 43.4925 Å2 / Biso min: 9.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.96→48.288 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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