SAXSdb — 1c4t

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

PROTEIN (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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 173–405 Chain B； UniProt 173–405 Chain C； UniProt 173–405	Fragment：CATALYTIC DOMAIN, RESIDUES 172 - 404	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

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 1C4T	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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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
1E2O CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE Deposited 1998-05-26	Different construct Different mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion 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
1SCZ Improved structural model for the catalytic domain of E.coli dihydrolipoamide succinyltransferase Deposited 2004-02-12	Different construct Different mutation/modification Different oligomeric state 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	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 oligomeric state Different ligand/ion 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 ligand/ion 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 173–405 Author chain B； PDBConstruct 1–233； UniProt 173–405 Author chain C； PDBConstruct 1–233； UniProt 173–405

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	1c4t
Deposition date deposition_date	1999-09-22
Structure title title	CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
Keywords keywords	TRANSFERASE, ACYLTRANSFERASE, KETOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX; 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	26.50 Å
Radius of gyration Rg (electron density) rg_electron	25.33 Å
Forward intensity I(0) i0	81951500.00
Molecular weight molecular_weight	71603.0 kDa
Excluded volume excluded_volume	90132 Å³
Envelope volume envelope_volume	111170 Å³
Hydration-shell volume shell_volume	35290 Å³
Envelope diameter envelope_diameter	85.2 Å
Shell Rg shell_rg	33.97 Å
Envelope Rg envelope_rg	25.61 Å
Shape Rg shape_rg	25.38 Å
Total Rg total_rg	26.14 Å
Total atoms total_atoms	5016
Residues n_residues	667
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	80.9 Å
Rg (real space) rg_real	26.33 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	8.1950e+07
I(0) uncertainty (real space) i0_real_error	1.0960e+06
Rg (reciprocal space) rg_reciprocal	26.39 Å
I(0) (reciprocal space) i0_reciprocal	81950000.0000
Solution quality estimate total_estimate	0.7425
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.7 Å
Skewness Skewness skewness	0.139
Kurtosis Kurtosis kurtosis	-0.500
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21080000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 0.291; Positv: 1.000; Valcen: 0.987; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (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	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5044

ARSEKRVPMTRLRKRVAERLLEAKNSTAMLTTFNEVNMKPIMDLRKQYGEAFEKRHGIRLGFMSFYVKAVVEALKRYPEVNASIDGDDVVYHNYFDVSMAVSTPRGLVTPVLRDVDTLGMADIEKKIKELAVKGRDGKLTVEDLTGGNFTITNGGVFGSLMSTPIINPPQSAILGMHAIKDRPMAVNGQVEILPMMYLALSYDHRLIDGRESVGFLVTIKELLEDPTRLLLDV

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	469008
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	28

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1c4ta_
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

Domain ID domain_id	d1c4tb_
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

Domain ID domain_id	d1c4tc_
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 (3 domains)

Domain ID domain_id	1c4tA00
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

Domain ID domain_id	1c4tB00
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

Domain ID domain_id	1c4tC00
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 (3)

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Unit-cell length a length_a	112.175 Å
Unit-cell length b length_b	112.175 Å
Unit-cell length c length_c	134.417 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2570
R_work r_work	0.2570
R_free r_free	0.2860

fit	/app/data/saxs_computation/c4/1c4t/1c4t.fit
pddf	/app/data/pr_computation/c4/1c4t/1c4t.pr.out
profile	/app/data/saxs_computation/c4/1c4t/1c4t.dat

CATALYTIC DOMAIN FROM TRIMERIC DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE

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

PROTEIN (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