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Yorodumi- PDB-2f5z: Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f5z | ||||||
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Title | Crystal Structure of Human Dihydrolipoamide Dehydrogenase (E3) Complexed to the E3-Binding Domain of Human E3-Binding Protein | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PROTEIN BINDING / protein-protein complex / OXIDOREDUCTASE-PROTEIN BINDING COMPLEX | ||||||
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 / acyltransferase activity / 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: 2.18 Å | ||||||
Authors | Brautigam, C.A. / Chuang, J.L. / Wynn, R.M. / Tomchick, D.R. / Machius, M. / Chuang, D.T. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Structural Insight into Interactions between Dihydrolipoamide Dehydrogenase (E3) and E3 Binding Protein of Human Pyruvate Dehydrogenase Complex. Authors: Brautigam, C.A. / Wynn, R.M. / Chuang, J.L. / Machius, M. / Tomchick, D.R. / Chuang, D.T. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1, 2, 3, 4, 5 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS ...BIOMOLECULE: 1, 2, 3, 4, 5 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 15CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS INDICATE THAT BIOMOLECULE 1 BEST REPRESENTS THE PHYSIOLOGICAL COMPLEX |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f5z.cif.gz | 977.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f5z.ent.gz | 807.8 KB | Display | PDB format |
PDBx/mmJSON format | 2f5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f5z ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f5z | HTTPS FTP |
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-Related structure data
Related structure data | 2f60C 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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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 50208.406 Da / Num. of mol.: 10 / Fragment: Dihydrolipoyl dehydrogenase, residues 36-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Plasmid: pTrcHisThE3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: P09622, dihydrolipoyl dehydrogenase #2: Protein | Mass: 7150.151 Da / Num. of mol.: 5 / Fragment: E3-binding domain, residues 173-230 / Mutation: K120G,T176L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDHX, PDX1 / Plasmid: pET-LTE3BD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: O00330 #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-FAD / #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: 3.35 Å3/Da / Density % sol: 63.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 14% (w/v) PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium acetate, 0.03 M spermidine, 8% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979426 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 9, 2004 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979426 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→37.4 Å / Num. all: 367237 / Num. obs: 367237 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.054 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 31492 / Rsym value: 0.401 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZMD without NADH Resolution: 2.18→37.4 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residues of E3BD with missing atoms were modeled as alanine due to missing density for the side chain
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Displacement parameters | Biso mean: 42.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.18→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.32 Å / Rfactor Rfree error: 0.012
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