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- PDB-1c4t: CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c4t | ||||||
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Title | CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE | ||||||
![]() | PROTEIN (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. / Carroll, D. / Lawson, J.E. / Ernst, S.R. / Reed, L.J. / Hackert, M.L. | ||||||
![]() | ![]() Title: Expression, purification, and structural analysis of the trimeric form of the catalytic domain of the Escherichia coli dihydrolipoamide succinyltransferase. Authors: Knapp, J.E. / Carroll, D. / Lawson, J.E. / Ernst, S.R. / Reed, L.J. / Hackert, M.L. #1: ![]() 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. #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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.8 KB | Display | ![]() |
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PDB format | ![]() | 99.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 396.4 KB | Display | ![]() |
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Full document | ![]() | 408.5 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e2oS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 26107.420 Da / Num. of mol.: 3 / 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 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.6 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MSC MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→10 Å / Num. obs: 18669 / % possible obs: 95.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 57.3 Å2 / Rsym value: 10.3 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 30.9 / % possible all: 93.5 |
Reflection | *PLUS Num. obs: 18677 / % possible obs: 95.8 % / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 93.5 % / Num. unique obs: 1798 / Rmerge(I) obs: 0.309 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E2O Resolution: 3→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 49.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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