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Yorodumi- PDB-2dne: Solution Structure of RSGI RUH-058, a lipoyl domain of human 2-ox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dne | ||||||
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Title | Solution Structure of RSGI RUH-058, a lipoyl domain of human 2-oxoacid dehydrogenase | ||||||
Components | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex | ||||||
Keywords | TRANSFERASE / Lipoyl domain / Lipoic acid / 2-oxoacid dehydrogenase / oxoacid dehydrogenase / Synthesis of acyl CoA / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle ...dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / acetyl-CoA biosynthetic process from pyruvate / : / pyruvate dehydrogenase complex / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / intracellular membrane-bounded organelle / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Ruhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution Structure of RSGI RUH-058, a lipoyl domain of human 2-oxoacid dehydrogenase Authors: Ruhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dne.cif.gz | 563.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dne.ent.gz | 468.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dne_validation.pdf.gz | 343.3 KB | Display | wwPDB validaton report |
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Full document | 2dne_full_validation.pdf.gz | 481.3 KB | Display | |
Data in XML | 2dne_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 2dne_validation.cif.gz | 58.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dne ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dne | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11259.563 Da / Num. of mol.: 1 Fragment: N-terminal domain of 2-oxoacid dehydrogenase, Lipoyl-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P050829-14 / Production host: Cell free synthesis References: UniProt: P10515, dihydrolipoyllysine-residue acetyltransferase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.09mM domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM NaCl / pH: 7.0 / Pressure: Ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |