[English] 日本語
Yorodumi- PDB-1eaf: ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eaf | ||||||
---|---|---|---|---|---|---|---|
Title | ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX | ||||||
Components | DIHYDROLIPOYL-TRANSACETYLASE | ||||||
Keywords | DIHYDROLIPOAMIDE ACETYLTRANSFERASE | ||||||
Function / homology | Function and homology information dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / glycolytic process Similarity search - Function | ||||||
Biological species | Azotobacter vinelandii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | ||||||
Authors | Mattevi, A. / Hol, W.G.J. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p). Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Teplyakov, A. / Hol, W.G. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Three-Dimensional Structure of Lipoamide Dehydrogenase from Pseudomonas Fluorescens at 2.8 Angstroms Resolution. Analysis of Redox and Thermostability Properties Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Van Berkel, W.J. / Hol, W.G. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Refined Crystal Structure of the Catalytic Domain of Dihydrolipoyl Transacetylase (E2P) from Azotobacter Vinelandii at 2.6 Angstroms Resolution Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Westphal, A.H. / De Kok, A. / Hol, W.G. #3: Journal: Biochemistry / Year: 1993 Title: Crystallographic Analysis of Substrate Binding and Catalysis in Dihydrolipoyl Transacetylase (E2P) Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Teplyakov, A. / Hol, W.G. | ||||||
History |
| ||||||
Remark 700 | SHEET SHEET A IS ACTUALLY A FOUR-STRANDED SHEET. IT CONTAINS TWO ADDITIONAL STRANDS A 3 ILE 409 PRO ...SHEET SHEET A IS ACTUALLY A FOUR-STRANDED SHEET. IT CONTAINS TWO ADDITIONAL STRANDS A 3 ILE 409 PRO 413 -1 A 4 THR 566 PHE 568 -1 FROM A THREEFOLD-RELATED SUBUNIT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1eaf.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1eaf.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 1eaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/1eaf ftp://data.pdbj.org/pub/pdb/validation_reports/ea/1eaf | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 24||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUE 575 IS A CIS PROLINE. |
-Components
#1: Protein | Mass: 26241.748 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azotobacter vinelandii (bacteria) References: UniProt: P10802, dihydrolipoyllysine-residue acetyltransferase |
---|---|
#2: Chemical | ChemComp-SO3 / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.7 % |
---|---|
Crystal grow | Details: THESE COORDINATES ARE FOR THE BINARY COMPLEX WITH HYDROGEN SULPHITE (HSO2OH-). THIS COMPLEX WAS OBTAINED BY SOAKING WITH LIPOAMIDE AND SODIUM DITHIONITE. THE RESULTING ELECTRON DENSITY DOES ...Details: THESE COORDINATES ARE FOR THE BINARY COMPLEX WITH HYDROGEN SULPHITE (HSO2OH-). THIS COMPLEX WAS OBTAINED BY SOAKING WITH LIPOAMIDE AND SODIUM DITHIONITE. THE RESULTING ELECTRON DENSITY DOES NOT INDICATE THAT LIPOAMIDE IS BOUND. ON THE OTHER HAND, AN EXTRA DENSITY PEAK IN THE CATALYTIC CENTER IS INTERPRETED AS HSO2OH-. THE LATTER MIGHT BE DERIVED FROM THE HYDROLYSIS OF DITHIONITE. SEE REF 3. |
Crystal grow | *PLUS pH: 7 / Method: unknown / Details: used macroseeding |
Components of the solutions | *PLUS Conc.: 16 %sat / Common name: ammonium sulfate |
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Num. obs: 21825 / Rmerge(I) obs: 0.094 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.6→10 Å / Rfactor Rwork: 0.198 / Rfactor obs: 0.198 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 6 Å / σ(F): 0 / Rfactor all: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|