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- PDB-8jdz: Crystal structure of mLDHD in complex with 2-keto-3-methylvaleric acid -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jdz | |||||||||
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Title | Crystal structure of mLDHD in complex with 2-keto-3-methylvaleric acid | |||||||||
![]() | Probable D-lactate dehydrogenase, mitochondrial | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jin, S. / Chen, X. / Yang, J. / Ding, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Lactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis. Authors: Jin, S. / Chen, X. / Yang, J. / Ding, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 80.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8jdbC ![]() 8jdcC ![]() 8jddC ![]() 8jdeC ![]() 8jdfC ![]() 8jdgC ![]() 8jdnC ![]() 8jdoC ![]() 8jdpC ![]() 8jdqC ![]() 8jdrC ![]() 8jdsC ![]() 8jdtC ![]() 8jduC ![]() 8jdvC ![]() 8jdxC ![]() 8jdyC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 50452.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q7TNG8, ![]() |
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#2: Chemical | ChemComp-FAD / ![]() |
#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-1QQ / ( |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion / Details: 4.0 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.56→41.03 Å / Num. obs: 73896 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Χ2: 0.98 / Net I/σ(I): 16.8 / Num. measured all: 962013 |
Reflection shell | Resolution: 1.56→1.6 Å / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 1.387 / Num. measured all: 58976 / Num. unique obs: 5430 / CC1/2: 0.686 / Rpim(I) all: 0.439 / Rrim(I) all: 1.456 / Χ2: 0.87 / Net I/σ(I) obs: 1.7 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→34.13 Å
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Refine LS restraints |
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LS refinement shell |
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