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- PDB-3nyf: Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nyf | ||||||
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Title | Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with Imino-Histidine | ||||||
![]() | D-Arginine Dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / D-Arginine Dehydrogenase / FAD / Imino-Histidine | ||||||
Function / homology | ![]() D-arginine dehydrogenase / D-amino-acid dehydrogenase activity / arginine metabolic process / arginine catabolic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fu, G. / Weber, I.T. | ||||||
![]() | ![]() Title: Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase. Authors: Fu, G. / Yuan, H. / Li, C. / Lu, C.D. / Gadda, G. / Weber, I.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.1 KB | Display | ![]() |
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PDB format | ![]() | 140.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3nycSC ![]() 3nyeC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q9HXE3, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-HHI / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 0.1M 2-(N-morpholino)-ethanesulfonic acid (MES) pH 6.5-7.0, 5% glycerol, 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: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 97110 / Num. obs: 97110 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rsym value: 0.049 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5814 / % possible all: 54.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3NYC Resolution: 1.3→10 Å / Num. parameters: 30605 / Num. restraintsaints: 36537 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: conjugage gradient minimization
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Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3330.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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