+Open data
-Basic information
Entry | Database: PDB / ID: 8jdt | |||||||||
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Title | Crystal structure of mLDHD in complex with 2-ketobutanoic acid | |||||||||
Components | Probable D-lactate dehydrogenase, mitochondrial | |||||||||
Keywords | OXIDOREDUCTASE / D-lactate dehydrogenase / LDHD / 2-hydroxyacid | |||||||||
Function / homology | Function and homology information D-lactate dehydrogenase (cytochrome) / D-lactate dehydrogenase (cytochrome) activity / lactate catabolic process / D-lactate dehydrogenase activity / Mitochondrial protein import / ATP biosynthetic process / FAD binding / flavin adenine dinucleotide binding / mitochondrial inner membrane / mitochondrion Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Jin, S. / Chen, X. / Yang, J. / Ding, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nat Commun / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jdt.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jdt.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 8jdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/8jdt ftp://data.pdbj.org/pub/pdb/validation_reports/jd/8jdt | HTTPS FTP |
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-Related structure data
Related structure data | 8jdbC 8jdcC 8jddC 8jdeC 8jdfC 8jdgC 8jdnC 8jdoC 8jdpC 8jdqC 8jdrC 8jdsC 8jduC 8jdvC 8jdxC 8jdyC 8jdzC C: citing same article (ref.) |
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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 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.) Mus musculus (house mouse) / Gene: Ldhd / Production host: Escherichia coli (E. coli) References: UniProt: Q7TNG8, D-lactate dehydrogenase (cytochrome) |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-2KT / |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.71 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å |
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: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→32.01 Å / Num. obs: 74388 / % possible obs: 99.6 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.105 / Χ2: 0.98 / Net I/σ(I): 14 / Num. measured all: 990622 |
Reflection shell | Resolution: 1.55→1.59 Å / % possible obs: 99 % / Redundancy: 13.6 % / Rmerge(I) obs: 1.345 / Num. measured all: 73557 / Num. unique obs: 5394 / CC1/2: 0.776 / Rpim(I) all: 0.372 / Rrim(I) all: 1.396 / Χ2: 0.91 / Net I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→32.01 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.97 / Stereochemistry target values: ML
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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: 1.55→32.01 Å
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Refine LS restraints |
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LS refinement shell |
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