SAXSdb — 1scz

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydrolipoamide Succinyltransferase

Escherichia coli

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 homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 172–404	Fragment：catalytic domain, residues 172-404	No other associated polymer	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

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 1SCZ	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	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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
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 Deposited 1992-02-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 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 ligand/ion 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 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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
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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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 1–233； UniProt 172–404

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1scz
Deposition date deposition_date	2004-02-12
Structure title title	Improved structural model for the catalytic domain of E.coli dihydrolipoamide succinyltransferase
Keywords keywords	CoA-dependent acyltransferase, CAT-like, alpha and beta (2 layers), mixed beta-sheeet of 6 strands, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.62 Å
Radius of gyration Rg (electron density) rg_electron	19.32 Å
Forward intensity I(0) i0	12051800.00
Molecular weight molecular_weight	26073.0 kDa
Excluded volume excluded_volume	32906 Å³
Envelope volume envelope_volume	42711 Å³
Hydration-shell volume shell_volume	18797 Å³
Envelope diameter envelope_diameter	74.5 Å
Shell Rg shell_rg	25.55 Å
Envelope Rg envelope_rg	20.44 Å
Shape Rg shape_rg	19.30 Å
Total Rg total_rg	20.38 Å
Total atoms total_atoms	1827
Residues n_residues	233
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	72.5 Å
Rg (real space) rg_real	20.64 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.2050e+07
I(0) uncertainty (real space) i0_real_error	1.6560e+05
Rg (reciprocal space) rg_reciprocal	20.63 Å
I(0) (reciprocal space) i0_reciprocal	12050000.0000
Solution quality estimate total_estimate	0.8492
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.2 Å
Skewness Skewness skewness	0.447
Kurtosis Kurtosis kurtosis	0.013
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1774000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.691; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1scza_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.43 — CoA-dependent acyltransferases
Superfamily Superfamily superfamily	c.43.1 — CoA-dependent acyltransferases
Family Family family	c.43.1.1 — CAT-like

CATH v4.4 (1 domains)

Domain ID domain_id	1sczA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	559 — Chloramphenicol Acetyltransferase
Homologous superfamily homologous superfamily	10 — Chloramphenicol acetyltransferase-like domain

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8. Citations (1)

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Unit-cell length a length_a	220.576 Å
Unit-cell length b length_b	220.576 Å
Unit-cell length c length_c	220.576 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	96

Space group space_group	F 4 3 2
Space-group number int_tables_number	209
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	19.890 Å
R factor r_factor	0.2140
R_work r_work	0.2110
R_free r_free	0.2340

Description description	Dihydrolipoamide Succinyltransferase
Molecular weight formula_weight	26107.4 kDa
EC 编号 ec_number	2.3.1.61
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2046

Improved structural model for the catalytic domain of E.coli dihydrolipoamide succinyltransferase

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydrolipoamide Succinyltransferase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	219

fit	/app/data/saxs_computation/sc/1scz/1scz.fit
pddf	/app/data/pr_computation/sc/1scz/1scz.pr.out
profile	/app/data/saxs_computation/sc/1scz/1scz.dat