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Yorodumi- PDB-3sm8: Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sm8 | ||||||
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Title | Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with an (N5) Flavin Adduct | ||||||
Components | FAD-dependent catabolic D-arginine dehydrogenase, DauA | ||||||
Keywords | OXIDOREDUCTASE / N(5) Flavin Adduct | ||||||
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: 1.07 Å | ||||||
Authors | Fu, G. / Weber, I.T. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Atomic-resolution structure of an N5 flavin adduct in D-arginine dehydrogenase. Authors: Fu, G. / Yuan, H. / Wang, S. / Gadda, G. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sm8.cif.gz | 180.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sm8.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 3sm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sm8_validation.pdf.gz | 681.9 KB | Display | wwPDB validaton report |
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Full document | 3sm8_full_validation.pdf.gz | 687.5 KB | Display | |
Data in XML | 3sm8_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 3sm8_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/3sm8 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/3sm8 | HTTPS FTP |
-Related structure data
Related structure data | 3yneS 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
#1: Protein | Mass: 41405.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: dauA, PA3863, PAO1 / Plasmid: pBAD-His-6 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 References: UniProt: Q9HXE3, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor | ||||
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#2: Chemical | #3: Chemical | ChemComp-FNK / [( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Crystals were grown by the hanging drop vapor diffusion method using a well solution of 0.1M 2-(N-morpholino)-ethanesulfonic acid (MES) pH 6.5-7.0, 5% glycerol, and 6-10% (w/v) PEG6000., ...Details: Crystals were grown by the hanging drop vapor diffusion method using a well solution of 0.1M 2-(N-morpholino)-ethanesulfonic acid (MES) pH 6.5-7.0, 5% glycerol, and 6-10% (w/v) PEG6000., VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→50 Å / Num. obs: 187536 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rsym value: 0.067 |
Reflection shell | Resolution: 1.07→1.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7585 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3YNE Resolution: 1.07→10 Å / Num. parameters: 30975 / Num. restraintsaints: 37435 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: conjugate gradient minimization
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Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3323.12 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→10 Å
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Refine LS restraints |
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