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Yorodumi- PDB-7vid: The crystal structure of L-leucine dehydrogenase from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vid | |||||||||
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Title | The crystal structure of L-leucine dehydrogenase from Pseudomonas aeruginosa | |||||||||
Components | Leucine dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Pseudomonas aeruginosa / PA3418 / leucine dehydrogenase / branched chain amino acid | |||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process / nucleotide binding Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Kim, S. / Kang, W. / Yang, J.K. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: Mol.Cells / Year: 2022 Title: The Crystal Structure of L-Leucine Dehydrogenase from Pseudomonas aeruginosa. Authors: Kim, S. / Koh, S. / Kang, W. / Yang, J.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vid.cif.gz | 161.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vid.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 7vid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/7vid ftp://data.pdbj.org/pub/pdb/validation_reports/vi/7vid | HTTPS FTP |
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-Related structure data
Related structure data | 1lehS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36500.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: ldh, PA3418 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HYI7 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12 % (w/v) polyethylene glycol 3,350, 0.1M sodium acetate trihydrate PH range: 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→90.2 Å / Num. obs: 28028 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 47.17 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.16 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4015 / CC1/2: 0.714 / Rrim(I) all: 1.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LEH Resolution: 2.5→76.22 Å / SU ML: 0.3493 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6254 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: 46.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→76.22 Å
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Refine LS restraints |
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LS refinement shell |
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