1l5j

CRYSTAL STRUCTURE OF E. COLI ACONITASE B.

Method: X-RAY DIFFRACTION

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

Aconitate hydratase 2

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACONITATE ION × 1 FE3-S4 CLUSTER × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACONITATE ION × 1 FE3-S4 CLUSTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACON2_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–865； UniProt 1–865 Author chain B； PDBConstruct 1–865； UniProt 1–865

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	1l5j
Deposition date deposition_date	2002-03-07
Structure title title	CRYSTAL STRUCTURE OF E. COLI ACONITASE B.
Keywords keywords	Molecular recognition, RNA binding, Citric acid cycle, HEAT-like domain, 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.

1l5j__assembly_1__model_1

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

Download this curve (.dat)

1l5j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1l5j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.55 Å
Rg (electron density)	27.89 Å
Total Rg	28.56 Å
Atom count	6571
Residues	862
Excluded volume	117360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1l5j__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1l5j__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Aconitate hydratase 2
Molecular weight formula_weight	93600.9 kDa
EC 编号 ec_number	4.2.1.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	13712

MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAAYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVVGTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDTYRYLNFNQLSQYTEKADGVIFQTAV

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	ACONITATE ION
Molecular weight formula_weight	171.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FE3-S4 CLUSTER
Molecular weight formula_weight	295.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	570

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1l5ja1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.15 — Aconitase B, N-terminal domain
Family Family family	a.118.15.1 — Aconitase B, N-terminal domain

Domain ID domain_id	d1l5ja2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.2 — LeuD/IlvD-like
Family Family family	c.8.2.1 — LeuD-like

Domain ID domain_id	d1l5ja3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.83 — Aconitase iron-sulfur domain
Superfamily Superfamily superfamily	c.83.1 — Aconitase iron-sulfur domain
Family Family family	c.83.1.1 — Aconitase iron-sulfur domain

Domain ID domain_id	d1l5jb1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.15 — Aconitase B, N-terminal domain
Family Family family	a.118.15.1 — Aconitase B, N-terminal domain

Domain ID domain_id	d1l5jb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.2 — LeuD/IlvD-like
Family Family family	c.8.2.1 — LeuD-like

Domain ID domain_id	d1l5jb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.83 — Aconitase iron-sulfur domain
Superfamily Superfamily superfamily	c.83.1 — Aconitase iron-sulfur domain
Family Family family	c.83.1.1 — Aconitase iron-sulfur domain

CATH v4.4 (10 domains)

Domain ID domain_id	1l5jA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	310 — Aconitate B, HEAT-like domain

Domain ID domain_id	1l5jA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	19 — Aconitase; domain 4
Homologous superfamily homologous superfamily	10 — Aconitase, domain 4

Domain ID domain_id	1l5jA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1060 — Aconitase; Domain 2
Homologous superfamily homologous superfamily	10 — Aconitase, Domain 2

Domain ID domain_id	1l5jA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

Domain ID domain_id	1l5jA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

Domain ID domain_id	1l5jB01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	310 — Aconitate B, HEAT-like domain

Domain ID domain_id	1l5jB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	19 — Aconitase; domain 4
Homologous superfamily homologous superfamily	10 — Aconitase, domain 4

Domain ID domain_id	1l5jB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1060 — Aconitase; Domain 2
Homologous superfamily homologous superfamily	10 — Aconitase, Domain 2

Domain ID domain_id	1l5jB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

Domain ID domain_id	1l5jB05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	499 — Aconitase; domain 3
Homologous superfamily homologous superfamily	10 — Aconitase, domain 3

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Unit-cell length a length_a	138.970 Å
Unit-cell length b length_b	169.630 Å
Unit-cell length c length_c	113.380 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	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1537
R_work r_work	0.1512
R_free r_free	0.2028

CRYSTAL STRUCTURE OF E. COLI ACONITASE B.

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

Aconitate hydratase 2

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

1l5j__assembly_1__model_1

1l5j__assembly_1__model_1 | I(q)

1l5j__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

CATH v4.4 (10 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF E. COLI ACONITASE B.

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

Aconitate hydratase 2

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

1l5j__assembly_1__model_1

1l5j__assembly_1__model_1 | I(q)

1l5j__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

CATH v4.4 (10 domains)

7. Citations (1)