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Yorodumi- PDB-6lpq: Crystal structure of human D-2-hydroxyglutarate dehydrogenase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lpq | |||||||||
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Title | Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-MAL) | |||||||||
Components | D-2-hydroxyglutarate dehydrogenase, mitochondrial | |||||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / FLAVOPROTEIN | |||||||||
Function / homology | Function and homology information D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / malate metabolic process / 2-oxoglutarate metabolic process / response to cobalt ion / protein metabolic process / response to manganese ion / response to zinc ion / FAD binding ...D-2-hydroxyglutarate dehydrogenase / (R)-2-hydroxyglutarate dehydrogenase activity / Interconversion of 2-oxoglutarate and 2-hydroxyglutarate / malate metabolic process / 2-oxoglutarate metabolic process / response to cobalt ion / protein metabolic process / response to manganese ion / response to zinc ion / FAD binding / mitochondrial matrix / mitochondrion / zinc ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Yang, J. / Zhu, H. / Ding, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Discov / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lpq.cif.gz | 192.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lpq.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/6lpq ftp://data.pdbj.org/pub/pdb/validation_reports/lp/6lpq | HTTPS FTP |
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-Related structure data
Related structure data | 6lpnSC 6lppC 6lptC 6lpuC 6lpxC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: D2HGDH, D2HGD / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N465, EC: 1.1.99.- #2: Chemical | #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
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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: 2.25 Å3/Da / Density % sol: 45.28 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 21823 / % possible obs: 95.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 36.26 Å2 / Rmerge(I) obs: 0.297 / Rpim(I) all: 0.132 / Rrim(I) all: 0.326 / Χ2: 0.461 / Net I/σ(I): 2.2 / Num. measured all: 132903 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LPN Resolution: 2.8→41.136 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.79 Å2 / Biso mean: 32.525 Å2 / Biso min: 12.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→41.136 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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