SAXSdb — 3abr

▼

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

Ethanolamine ammonia-lyase heavy chain

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Ethanolamine ammonia-lyase light chain × 6 （P19636） GLYCEROL × 18 SODIUM ION × 21 COBALAMIN × 6 water × 12	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Ethanolamine ammonia-lyase light chain × 2 （P19636） GLYCEROL × 6 SODIUM ION × 7 COBALAMIN × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EUTB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–453； UniProt 1–453 Author chain C； PDBConstruct 1–453； UniProt 1–453

Ethanolamine ammonia-lyase light chain

Escherichia coli

UniProt P19636

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Ethanolamine ammonia-lyase heavy chain × 6 （P0AEJ6） GLYCEROL × 18 SODIUM ION × 21 COBALAMIN × 6 water × 12	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Ethanolamine ammonia-lyase heavy chain × 2 （P0AEJ6） GLYCEROL × 6 SODIUM ION × 7 COBALAMIN × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EUTC_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 12–306； UniProt 1–295 Author chain D； PDBConstruct 12–306； UniProt 1–295

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3abr
Deposition date deposition_date	2009-12-21
Structure title title	Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)
Keywords keywords	(beta/alpha)8 fold, Cobalt, Lyase, Cobalamin; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3abr__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3abr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3abr__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	51.81 Å
Rg (electron density)	51.69 Å
Total Rg	51.99 Å
Atom count	32955
Residues	4230
Excluded volume	587390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3abr__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3abr__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Ethanolamine ammonia-lyase heavy chain
Molecular weight formula_weight	49447.8 kDa
EC 编号 ec_number	4.3.1.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	11985

MKLKTTLFGNVYQFKDVKEVLAKANELRSGDVLAGVAAASSQERVAAKQVLSEMTVADIRNNPVIAYEDDCVTRLIQDDVNETAYNQIKNWSISELREYVLSDETSVDDIAFTRKGLTSEVVAAVAKICSNADLIYGAKKMPVIKKANTTIGIPGTFSARLQPNDTRDDVQSIAAQIYEGLSFGVGDAVIGVNPVTDDVENLSRVLDTIYGVIDKFNIPTQGCVLAHVTTQIEAIRRGAPGGLIFQSICGSEKGLKEFGVELAMLDEARAVGAEFNRIAGENCLYFETGQGSALSAGANFGADQVTMEARNYGLARHYDPFIVNTVVGFIGPEYLYNDRQIIRAGLEDHFMGKLSGISMGCDCCYTNHADADQNLNENLMILLATAGCNYIMGMPLGDDIMLNYQTTAFHDTATVRQLLNLRPSPEFERWLESMGIMANGRLTKRAGDPSLFF

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ethanolamine ammonia-lyase light chain
Molecular weight formula_weight	33197.0 kDa
EC 编号 ec_number	4.3.1.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MDQSSHHHHHHMDQKQIEEIVRSVMASMGQAAPAPSEAKCATTNCAAPVTSESCALDLGSAEAKAWIGVENPHRADVLTELRRSTVARVCTGRAGPRPRTQALLRFLADHSRSKDTVLKEVPEEWVKAQGLLEVRSEISDKNLYLTRPDMGRRLCAEAVEALKAQCVANPDVQVVISDGLSTDAITVNYEEILPPLMAGLKQAGLKVGTPFFVRYGRVKIEDQIGEILGAKVVILLVGERPGLGQSESLSCYAVYSPRMATTVEADRTCISNIHQGGTPPVEAAAVIVDLAKRMLEQKASGINMTR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1000

▼

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3abrA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	170 — Ribosomal Protein L24e; Chain: T;
Homologous superfamily homologous superfamily	30 — ethanolamine ammonia-lyase heavy chain domain like

Domain ID domain_id	3abrA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	70 — lyase

Domain ID domain_id	3abrA03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3abrB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	40 — Ethanolamine ammonia-lyase light chain (EutC), N-terminal domain

Domain ID domain_id	3abrB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11240 — Ethanolamine ammonia-lyase light chain (EutC)

Domain ID domain_id	3abrC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	170 — Ribosomal Protein L24e; Chain: T;
Homologous superfamily homologous superfamily	30 — ethanolamine ammonia-lyase heavy chain domain like

Domain ID domain_id	3abrC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	70 — lyase

Domain ID domain_id	3abrC03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	3abrD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily	40 — Ethanolamine ammonia-lyase light chain (EutC), N-terminal domain

Domain ID domain_id	3abrD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11240 — Ethanolamine ammonia-lyase light chain (EutC)

▶

Unit-cell length a length_a	244.120 Å
Unit-cell length b length_b	244.120 Å
Unit-cell length c length_c	77.150 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	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	42.290 Å
R factor r_factor	0.2496
R_work r_work	0.2477
R_free r_free	0.2852

Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)

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

Ethanolamine ammonia-lyase heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Ethanolamine ammonia-lyase light chain

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3abr__assembly_1__model_1

3abr__assembly_1__model_1 | I(q)

3abr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl (substrate-free form)

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

Ethanolamine ammonia-lyase heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ethanolamine ammonia-lyase light chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3abr__assembly_1__model_1

3abr__assembly_1__model_1 | I(q)

3abr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)