+
Open data
-
Basic information
Entry | Database: PDB / ID: 1e2o | ||||||
---|---|---|---|---|---|---|---|
Title | CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE | ||||||
![]() | DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE | ||||||
![]() | TRANSFERASE / ACYLTRANSFERASE / KETOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX | ||||||
Function / homology | ![]() L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / lipoic acid binding / tricarboxylic acid cycle / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Knapp, J.E. / Mitchell, D.T. / Yazdi, M.A. / Ernst, S.R. / Reed, L.J. / Hackert, M.L. | ||||||
![]() | ![]() Title: Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex. Authors: Knapp, J.E. / Mitchell, D.T. / Yazdi, M.A. / Ernst, S.R. / Reed, L.J. / Hackert, M.L. #1: ![]() Title: Atomic Structure of the Cubic Core of the Pyruvate Dehydrogenase Multienzyme Complex Authors: Mattevi, A. / Obmolova, G. / Schulze, E. / Kalk, K.H. / Westphal, A.H. / De Kok, A. / Hol, W.G. #2: ![]() Title: Nucleotide Sequence of the Sucb Gene Encoding the Dihydrolipoamide Succinyltransferase of Escherichia Coli K12 and Homology with the Corresponding Acetyltransferase Authors: Spencer, M.E. / Darlison, M.G. / Stephens, P.E. / Duckenfield, I.K. / Guest, J.R. #3: ![]() Title: Crystallization and Preliminary Structural Analysis of Dihydrolipoyl Transsuccinylase, the Core of the 2-Oxoglutarate Dehydrogenase Complex Authors: Derosier, D.J. / Oliver, R.M. / Reed, L.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 52.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 372.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 375.1 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eaaS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 24||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 26107.420 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 172 - 404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P07016, UniProt: P0AFG6*PLUS, dihydrolipoyllysine-residue succinyltransferase |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 1% ETHANOL, 50 MM POTASSIUM PHOSPHATE, PH 7.0 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 9906 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rsym value: 0.046 / Net I/σ(I): 13 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.145 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.145 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EAA Resolution: 3→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL AND RESOLUTION-DEPENDENT WEIGHTING SCHEME USED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|