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1bbl

THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE E3-BINDING DOMAIN OF THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE CORE FROM THE 2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX OF ESCHERICHIA COLI

Method: SOLUTION NMR Dmax: 35.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE

Escherichia coli

UniProt P07016

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 103–152 Not recorded No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1BBL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BAL THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE E3-BINDING DOMAIN OF THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE CORE FROM THE 2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX OF (ESCHERICHIA COLI) Deposited 1992-02-20 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 103–152（50 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1C4T CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE Deposited 1999-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 173–405（233 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 172 - 404
Chain B 173–405（233 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 172 - 404
Chain C 173–405（233 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 172 - 404
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 3.00 Å R-free 0.286
1E2O CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE Deposited 1998-05-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 172–404（233 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 172 - 404
Not recorded SO4 SULFATE ION × 24 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 1% ETHANOL, 50 MM POTASSIUM PHOSPHATE, PH 7.0
Resolution 3.00 Å R-free 0.249
1PMR LIPOYL DOMAIN FROM THE DIHYDROLIPOYL SUCCINYLTRANSFERASE COMPONENT OF THE 2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX OF ESCHERICHIA COLI, NMR, 25 STRUCTURES Deposited 1997-07-24 Different construct Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–80（80 aa） Fragment：LIPOYL DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1SCZ Improved structural model for the catalytic domain of E.coli dihydrolipoamide succinyltransferase Deposited 2004-02-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 172–404（233 aa） Fragment：catalytic domain, residues 172-404
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；5% PEG 4000,0.05M Hepes, 0.2M Ammonium acetate, 0.15M Magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.20 Å R-free 0.234
2BTG peripheral-subunit binding domains from mesophilic,thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions Deposited 2005-05-31 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–152（45 aa） Fragment：RESIDUES 108-152
Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K
NMR sample composition 50 MM POTASSIUM PHOSPHATE, 10% D2O
Resolution not provided
2BTH Peripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state transitions Deposited 2005-05-31 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 108–152（45 aa） Fragment：RESIDUES 108-152
Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K
NMR sample composition 50 MM POTASSIUM PHOSPHATE, 10% D2
Resolution not provided

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ODO2_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–51； UniProt 103–152

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1bbl

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bbl
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bbl
Deposition date deposition_date1992-02-20
Structure title titleTHREE-DIMENSIONAL SOLUTION STRUCTURE OF THE E3-BINDING DOMAIN OF THE DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE CORE FROM THE 2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX OF ESCHERICHIA COLI
Keywords keywordsGLYCOLYSIS; GLYCOLYSIS
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier11.44 Å
Radius of gyration Rg (electron density) rg_electron9.79 Å
Forward intensity I(0) i0469619.00
Molecular weight molecular_weight3979.0 kDa
Excluded volume excluded_volume4959 ų
Envelope volume envelope_volume6174 ų
Hydration-shell volume shell_volume5895 ų
Envelope diameter envelope_diameter32.7 Å
Shell Rg shell_rg14.28 Å
Envelope Rg envelope_rg9.98 Å
Shape Rg shape_rg9.77 Å
Total Rg total_rg11.40 Å
Total atoms total_atoms573
Residues n_residues37
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax35.8 Å
Rg (real space) rg_real11.36 Å
Rg uncertainty (real space) rg_real_error0.21 Å
I(0) (real space) i0_real4.6960e+05
I(0) uncertainty (real space) i0_real_error4.7240e+03
Rg (reciprocal space) rg_reciprocal11.37 Å
I(0) (reciprocal space) i0_reciprocal469600.0000
Solution quality estimate total_estimate0.8929
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.8 Å
Skewness Skewness skewness0.031
Kurtosis Kurtosis kurtosis-0.337
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52690.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.973
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1bbla_
Class classa — All alpha proteins
Fold Fold folda.9 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Superfamily Superfamily superfamilya.9.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
Family Family familya.9.1.1 — Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
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8. Citations (1)

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9. Files and Curves (10)