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Yorodumi- PDB-3rnm: The crystal structure of the subunit binding of human dihydrolipo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rnm | ||||||
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Title | The crystal structure of the subunit binding of human dihydrolipoamide transacylase (E2b) bound to human dihydrolipoamide dehydrogenase (E3) | ||||||
Components |
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Keywords | OXIDOREDUCTASE/PROTEIN BINDING / protein-protein interaction / redox protein / mitochondrion / OXIDOREDUCTASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity / acetyltransferase complex / acrosomal matrix / Glycine degradation / : / oxoglutarate dehydrogenase complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : ...dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity / acetyltransferase complex / acrosomal matrix / Glycine degradation / : / oxoglutarate dehydrogenase complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : / Lysine catabolism / acetyl-CoA biosynthetic process from pyruvate / lipoic acid binding / 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 nucleoid / mitochondrial electron transport, NADH to ubiquinone / acetyltransferase activity / RHOH GTPase cycle / gastrulation / regulation of membrane potential / microtubule cytoskeleton / flavin adenine dinucleotide binding / mitochondrial matrix / ubiquitin protein ligase binding / mitochondrion / proteolysis / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Authors | Brautigam, C.A. / Wynn, R.M. / Chuang, J.C. / Young, B.B. / Chuang, D.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural and Thermodynamic Basis for Weak Interactions between Dihydrolipoamide Dehydrogenase and Subunit-binding Domain of the Branched-chain {alpha}-Ketoacid Dehydrogenase Complex. Authors: Brautigam, C.A. / Wynn, R.M. / Chuang, J.L. / Naik, M.T. / Young, B.B. / Huang, T.H. / Chuang, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rnm.cif.gz | 744.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rnm.ent.gz | 635.1 KB | Display | PDB format |
PDBx/mmJSON format | 3rnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/3rnm ftp://data.pdbj.org/pub/pdb/validation_reports/rn/3rnm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Chains A, B, and E / Chains C, D, and F |
-Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 52652.137 Da / Num. of mol.: 4 / Fragment: Residues 36-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DLD, GCSL, LAD, PHE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P09622, dihydrolipoyl dehydrogenase #2: Protein | Mass: 6592.526 Da / Num. of mol.: 2 / Fragment: subunit-binding domain, residues 165-213 / Mutation: R118N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DBT, BCATE2 / Production host: Escherichia coli (E. coli) References: UniProt: P11182, dihydrolipoyllysine-residue (2-methylpropanoyl)transferase |
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-Non-polymers , 4 types, 359 molecules
#3: Chemical | ChemComp-BME / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-NHE / #6: 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: 2.58 Å3/Da / Density % sol: 52.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.1 Details: 18% PEG3350 0.1 M CHES , pH 9.1, 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: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2010 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 88688 / Num. obs: 88688 / % possible obs: 100 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→44.872 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 25.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.59 Å2 / ksol: 0.309 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→44.872 Å
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Refine LS restraints |
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LS refinement shell |
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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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