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- PDB-6lpn: Crystal structure of human D-2-hydroxyglutarate dehydrogenase in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6lpn | |||||||||
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Title | Crystal structure of human D-2-hydroxyglutarate dehydrogenase in apo form | |||||||||
![]() | D-2-hydroxyglutarate dehydrogenase, mitochondrial | |||||||||
![]() | OXIDOREDUCTASE / dehydrogenase / FLAVOPROTEIN | |||||||||
Function / homology | ![]() D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / : / 2-oxoglutarate metabolic process / malate metabolic process / response to cobalt ion / protein metabolic process / response to manganese ion / response to zinc ion ...D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / : / 2-oxoglutarate metabolic process / malate metabolic process / response to cobalt ion / protein metabolic process / response to manganese ion / response to zinc ion / respiratory electron transport chain / FAD binding / mitochondrial matrix / mitochondrion / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Yang, J. / Zhu, H. / Ding, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations. Authors: Yang, J. / Zhu, H. / Zhang, T. / 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 | ![]() | 378.4 KB | Display | ![]() |
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PDB format | ![]() | 304.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38.5 KB | Display | |
Data in CIF | ![]() | 56.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lppC ![]() 6lpqC ![]() 6lptC ![]() 6lpuC ![]() 6lpxC ![]() 3pm9S 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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Unit cell |
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Components
#1: Protein | Mass: 52332.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BIS-TRIS, pH 6.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 45047 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.95 Å2 / Rmerge(I) obs: 0.269 / Rpim(I) all: 0.112 / Rrim(I) all: 0.292 / Χ2: 1.363 / Net I/σ(I): 2.8 / Num. measured all: 299485 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PM9 Resolution: 2.206→39.834 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.64 Å2 / Biso mean: 31.3427 Å2 / Biso min: 10.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.206→39.834 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -0.435 Å / Origin y: -18.869 Å / Origin z: 43.829 Å
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Refinement TLS group |
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