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Yorodumi- PDB-7rdf: Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rdf | ||||||
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Title | Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine | ||||||
Components | FAD-dependent catabolic D-arginine dehydrogenase DauA | ||||||
Keywords | FLAVOPROTEIN / Flavin versatility / Flavin N5 adduct / 6-OH-FAD / D-arginine Dehydrogenase / ligand identity | ||||||
Function / homology | Function and homology information D-arginine dehydrogenase / D-amino-acid dehydrogenase activity / arginine metabolic process / arginine catabolic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Reis, R.A.G. / Iyer, A. / Agniswamy, A. / Weber, I.T. / Gadda, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2021 Title: Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase. Authors: Iyer, A. / Reis, R.A.G. / Agniswamy, J. / Weber, I.T. / Gadda, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rdf.cif.gz | 238.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rdf.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rdf_validation.pdf.gz | 944.4 KB | Display | wwPDB validaton report |
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Full document | 7rdf_full_validation.pdf.gz | 953.4 KB | Display | |
Data in XML | 7rdf_validation.xml.gz | 22 KB | Display | |
Data in CIF | 7rdf_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/7rdf ftp://data.pdbj.org/pub/pdb/validation_reports/rd/7rdf | HTTPS FTP |
-Related structure data
Related structure data | 3nyeS S: Starting model for refinement |
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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, 1 molecules A
#1: Protein | Mass: 40594.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: dauA, PA3863 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXE3, D-arginine dehydrogenase |
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-Non-polymers , 5 types, 408 molecules
#2: Chemical | ChemComp-4R2 / [[( | ||||
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#3: Chemical | ChemComp-6FA / | ||||
#4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-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: 2.17 Å3/Da / Density % sol: 43.2 % / Description: Green-colored pyramidal crystals |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 13% (w/v) PEG 3350, 6% (w/v) PEG 6000, 20 mM TRIS-Cl, pH 7.0, 10% glycerol, 5 mM D-arginine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→47.28 Å / Num. obs: 86350 / % possible obs: 97.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 11.94 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.03159 / Rsym value: 0.086 / Net I/σ(I): 16.35 |
Reflection shell | Resolution: 1.29→1.36 Å / Rmerge(I) obs: 0.1497 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 11210 / CC1/2: 0.906 / Rsym value: 0.0357 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NYE Resolution: 1.29→40.19 Å / SU ML: 0.0926 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.3488 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 17.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→40.19 Å
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Refine LS restraints |
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LS refinement shell |
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