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Open data
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Basic information
Entry | Database: PDB / ID: 8jdc | |||||||||
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Title | Crystal structure of mLDHD in apo form | |||||||||
![]() | Probable D-lactate dehydrogenase, mitochondrial | |||||||||
![]() | OXIDOREDUCTASE / D-lactate dehydrogenase / LDHD / 2-hydroxyacid | |||||||||
Function / homology | ![]() D-lactate dehydrogenase (cytochrome) / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / Mitochondrial protein import / D-lactate dehydrogenase activity / ATP biosynthetic process / Mitochondrial protein degradation / FAD binding / flavin adenine dinucleotide binding / mitochondrial inner membrane / mitochondrion 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 | ![]() | 107.8 KB | Display | ![]() |
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PDB format | ![]() | 79 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 780.3 KB | Display | ![]() |
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Full document | ![]() | 782.9 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jdbC ![]() 8jddC ![]() 8jdeC ![]() 8jdfC ![]() 8jdgC ![]() 8jdnC ![]() 8jdoC ![]() 8jdpC ![]() 8jdqC ![]() 8jdrC ![]() 8jdsC ![]() 8jdtC ![]() 8jduC ![]() 8jdvC ![]() 8jdxC ![]() 8jdyC ![]() 8jdzC 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, D-lactate dehydrogenase (cytochrome) |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.83 % |
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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 EIGER2 S 9M / Detector: PIXEL / Date: Nov 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.696→78.93 Å / Num. obs: 51046 / % possible obs: 88.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.021 / Rrim(I) all: 0.058 / Χ2: 0.91 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.7→1.79 Å / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.672 / Num. measured all: 52341 / Num. unique obs: 8242 / CC1/2: 0.844 / Rpim(I) all: 0.284 / Rrim(I) all: 0.731 / Χ2: 0.68 / Net I/σ(I) obs: 2.8 |
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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: 1.696→31.682 Å
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Refine LS restraints |
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LS refinement shell |
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