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- PDB-6p9d: Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6p9d | ||||||
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Title | Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F variant with FAD - Yellow fraction | ||||||
![]() | FAD-dependent catabolic D-arginine dehydrogenase DauA | ||||||
![]() | FLAVOPROTEIN / Oxidoreductase / Dehydrogenase Pseudomonas aeruginosa 6-OH-FAD D-amino acids | ||||||
Function / homology | ![]() D-arginine dehydrogenase / D-amino-acid dehydrogenase activity / arginine metabolic process / arginine catabolic process / oxidoreductase activity / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reis, R.A.G. / Iyer, A. / Agniswamy, J. / Gannavaram, S. / Weber, I. / Gadda, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity. Authors: Iyer, A. / Reis, R.A.G. / Gannavaram, S. / Momin, M. / Spring-Connell, A.M. / Orozco-Gonzalez, Y. / Agniswamy, J. / Hamelberg, D. / Weber, I.T. / Gozem, S. / Wang, S. / Germann, M.W. / Gadda, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.7 KB | Display | ![]() |
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PDB format | ![]() | 154.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 725.8 KB | Display | ![]() |
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Full document | ![]() | 728.5 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pldC ![]() 3nyeS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 40594.715 Da / Num. of mol.: 1 / Mutation: Y249F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: dauA, PA3863 / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FDA / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05 M Tris-Cl pH 7.0-7.3, 10% glycerol, and 12-13% (w/v) PEG 3350, 5-10% PEG 6000 PH range: 7.0-7.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.329→39.95 Å / Num. obs: 79369 / % possible obs: 99.37 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.01957 / Net I/σ(I): 17.19 |
Reflection shell | Resolution: 1.329→1.377 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 7650 / CC1/2: 0.882 / % possible all: 96.96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NYE Resolution: 1.329→37.01 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.329→37.01 Å
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LS refinement shell | Resolution: 1.329→1.3446 Å /
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