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Yorodumi- PDB-5j5z: Crystal structure of the D444V disease-causing mutant of the huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j5z | ||||||||||||||||||
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Title | Crystal structure of the D444V disease-causing mutant of the human dihydrolipoamide dehydrogenase | ||||||||||||||||||
Components | Dihydrolipoyl dehydrogenase, mitochondrialDihydrolipoamide dehydrogenase | ||||||||||||||||||
Keywords | OXIDOREDUCTASE / dihydrolipoamide dehydrogenase / E3 subunit / disease-causing mutant / E3 deficiency | ||||||||||||||||||
Function / homology | Function and homology information acetyltransferase complex / acrosomal matrix / Glycine degradation / : / oxoglutarate dehydrogenase complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : / Lysine catabolism / acetyl-CoA biosynthetic process from pyruvate ...acetyltransferase complex / acrosomal matrix / Glycine degradation / : / oxoglutarate dehydrogenase complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : / Lysine catabolism / acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / branched-chain amino acid catabolic process / : / Citric acid cycle (TCA cycle) / Branched-chain amino acid catabolism / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / motile cilium / sperm capacitation / Signaling by Retinoic Acid / mitochondrial electron transport, NADH to ubiquinone / gastrulation / regulation of membrane potential / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / proteolysis / nucleus Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||||||||||||||
Authors | Szabo, E. / Mizsei, R. / Zambo, Z. / Torocsik, B. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A. | ||||||||||||||||||
Funding support | Hungary, 5items
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Citation | Journal: Free Radic. Biol. Med. / Year: 2018 Title: Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase. Authors: Szabo, E. / Mizsei, R. / Wilk, P. / Zambo, Z. / Torocsik, B. / Weiss, M.S. / Adam-Vizi, V. / Ambrus, A. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j5z.cif.gz | 382.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j5z.ent.gz | 308.7 KB | Display | PDB format |
PDBx/mmJSON format | 5j5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/5j5z ftp://data.pdbj.org/pub/pdb/validation_reports/j5/5j5z | HTTPS FTP |
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-Related structure data
Related structure data | 5nhgC 1zmdS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 52621.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Plasmid: pET52b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09622, dihydrolipoyl dehydrogenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: reservoir solution: 1.6 M NaH2PO4/K2HPO4 buffer, pH 8.1 (K2HPO4 was titrated with NaH2PO4 to pH 8.1) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2015 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→48.38 Å / Num. obs: 105160 / % possible obs: 98.1 % / Redundancy: 4.54 % / Biso Wilson estimate: 36.45 Å2 / Net I/av σ(I): 50.85 / Net I/σ(I): 10.78 |
Reflection shell | Resolution: 1.84→1.95 Å / Mean I/σ(I) obs: 0.87 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZMD Resolution: 1.84→48.38 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.562 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.116 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.7 Å2 / Biso mean: 39.357 Å2 / Biso min: 18.11 Å2
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Refinement step | Cycle: final / Resolution: 1.84→48.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.887 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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