2qez

Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution

Method: X-RAY DIFFRACTION

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

Ethanolamine ammonia-lyase heavy chain

Listeria monocytogenes serotype 4b

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	GLYCEROL × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 3 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q720Q3_LISMF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–455； UniProt 1–454 Author chain B； PDBConstruct 2–455； UniProt 1–454 Author chain C； PDBConstruct 2–455； UniProt 1–454 Author chain D； PDBConstruct 2–455； UniProt 1–454 Author chain E； PDBConstruct 2–455； UniProt 1–454 Author chain F； PDBConstruct 2–455； UniProt 1–454

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	2qez
Deposition date deposition_date	2007-06-26
Structure title title	Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution
Keywords keywords	;YP_013784.1, ethanolamine ammonia-lyase heavy chain, Ethanolamine ammonia lyase large subunit (EutB), Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, LYASE ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

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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.

2qez__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2qez__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qez__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	29.61 Å
Rg (electron density)	28.54 Å
Total Rg	29.27 Å
Atom count	6508
Residues	844
Excluded volume	115440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qez__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qez__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2qez__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2qez__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ethanolamine ammonia-lyase heavy chain
Molecular weight formula_weight	50682.9 kDa
EC 编号 ec_number	4.3.1.7
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	20573

GMILKTNLFGHTYQFKSITDVLAKANEEKSGDRLAGVAAESAEERVAAKVVLSKMTLGDLRNNPVVPYETDEVTRIIQDQVNDRIHDSIKNWTVEELREWILDHKTTDADIKRVARGLTSEIIAAVTKLMSNLDLIYGAKKIRVIAHANTTIGLPGTFSARLQPNHPTDDPDGILASLMEGLTYGIGDAVIGLNPVDDSTDSVVRLLNKFEEFRSKWDVPTQTCVLAHVKTQMEAMRRGAPTGLVFQSIAGSEKGNTAFGFDGATIEEARQLALQSGAATGPNVMYFETGQGSELSSDAHFGVDQVTMEARCYGFAKKFDPFLVNTVVGFIGPEYLYDSKQVIRAGLEDHFMGKLTGISMGCDVCYTNHMKADQNDVENLSVLLTAAGCNFIMGIPHGDDVMLNYQTTGYHETATLRELFGLKPIKEFDQWMEKMGFSENGKLTSRAGDASIFLK

Source Source

Source organism organism	Listeria monocytogenes serotype 4b
NCBI taxonomy ID ncbi_taxonomy_id	265669
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	754

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	2qezA01
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	2qezA02
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	2qezA03
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	2qezB01
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	2qezB02
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	2qezB03
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	2qezC01
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	2qezC02
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	2qezC03
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	2qezD01
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	2qezD02
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	2qezD03
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	2qezE01
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	2qezE02
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	2qezE03
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	2qezF01
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	2qezF02
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	2qezF03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	188.330 Å
Unit-cell length b length_b	223.700 Å
Unit-cell length c length_c	65.930 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	24

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	29.210 Å
R factor r_factor	0.2300
R_work r_work	0.2280
R_free r_free	0.2790

Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2qez__assembly_4__model_1

2qez__assembly_4__model_1 | I(q)

2qez__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)

Crystal structure of ethanolamine ammonia-lyase heavy chain (YP_013784.1) from Listeria monocytogenes 4b F2365 at 2.15 A resolution

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2qez__assembly_4__model_1

2qez__assembly_4__model_1 | I(q)

2qez__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)