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Yorodumi- PDB-7fgp: Crystal structure of Aureimonas altamirenisis flavin-containing o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fgp | ||||||
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Title | Crystal structure of Aureimonas altamirenisis flavin-containing opine dehydrogenase (FAD-bound form) | ||||||
Components | Glycine/D-amino acid oxidase | ||||||
Keywords | FLAVOPROTEIN / Opine / Nopaline / Glycine oxidase family | ||||||
Function / homology | FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / oxidoreductase activity / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Glycine/D-amino acid oxidase Function and homology information | ||||||
Biological species | Aureimonas altamirensis DSM 21988 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å | ||||||
Authors | Yoshiwara, K. / Watanabe, Y. / Watanabe, S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structural basis for Flavin-containing opine dehydrogenase from Aureimonas altamirensis Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fgp.cif.gz | 175.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fgp.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 7fgp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/7fgp ftp://data.pdbj.org/pub/pdb/validation_reports/fg/7fgp | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42050.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aureimonas altamirensis DSM 21988 (bacteria) Gene: SAMN02745911_3969 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M6P181 |
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-Non-polymers , 5 types, 939 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.52 Å3/Da / Density % sol: 51.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Lithium sulfate, 0.1 M Bis-tris pH 5.5, 24.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.47→49.02 Å / Num. obs: 146819 / % possible obs: 100 % / Redundancy: 68.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.635 / Rpim(I) all: 0.076 / Rrim(I) all: 0.64 / Net I/σ(I): 10.1 / Num. measured all: 10079189 / Scaling rejects: 95628 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.47→49.018 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.73 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.05 Å2 / Biso mean: 20.9636 Å2 / Biso min: 6.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.47→49.018 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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