2ahu

Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.

Method: X-RAY DIFFRACTION

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

putative enzyme ydiF

Escherichia coli

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8X5X6_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–531； UniProt 1–531 Author chain B； PDBConstruct 1–531； UniProt 1–531 Author chain C； PDBConstruct 1–531； UniProt 1–531 Author chain D； PDBConstruct 1–531； UniProt 1–531

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	2ahu
Deposition date deposition_date	2005-07-28
Structure title title	Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.
Keywords keywords	;YdiF, CoA transferase, Glutamyl thioester, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, TRANSFERASE ;; TRANSFERASE
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.

2ahu__assembly_1__model_1

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

Download this curve (.dat)

2ahu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ahu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.81 Å
Rg (electron density)	40.47 Å
Total Rg	40.72 Å
Atom count	15696
Residues	2020
Excluded volume	282130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ahu__assembly_1__model_1`	tetrameric （4）	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 (2)

Entity 1 Entity 1 polymer

Description description	putative enzyme ydiF
Molecular weight formula_weight	58082.8 kDa
EC 编号 ec_number	2.8.3.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16967

MKPVKPPRINGRVPVLSAQEAVNYIPDEATLCVLGAGGGILEATTLITALADKYKQTQTPRNLSIISPTGLGDRADRGISPLAQEGLVKWALCGHWGQSPRISDLAEQNKIIAYNYPQGVLTQTLRAAAAHQPGIISDIGIGTFVDPRQQGGKLNEVTKEDLIKLVEFDNKEYLYYKAIAPDIAFIRATTCDSEGYATFEDEVMYLDALVIAQAVHNNGGIVMMQVQKMVKKATLHPKSVRIPGYLVDIVVVDPDQSQLYGGAPVNRFISGDFTLDDSTKLSLPLNQRKLVARRALFEMRKGAVGNVGVGIADGIGLVAREEGCADDFILTVETGPIGGITSQGIAFGANVNTRAILDMTSQFDFYHGGGLDVCYLSFAEVDQHGNVGVHKFNGKIMGTGGFIDISATSKKIIFCGTLTAGSLKTEIADGKLNIVQEGRVKKFIRELPEITFSGKIALERGLDVRYITERAVFTLKEDGLHLIEIAPGVDLQKDILDKMDFTPVISPELKLMDERLFIDAAMGFVLPEAAH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1271

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2ahua1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

Domain ID domain_id	d2ahua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

Domain ID domain_id	d2ahub1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

Domain ID domain_id	d2ahub2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

Domain ID domain_id	d2ahuc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

Domain ID domain_id	d2ahuc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

Domain ID domain_id	d2ahud1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.3 — CoA transferase beta subunit-like

Domain ID domain_id	d2ahud2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.124 — NagB/RpiA/CoA transferase-like
Superfamily Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
Family Family family	c.124.1.2 — CoA transferase alpha subunit-like

CATH v4.4 (8 domains)

Domain ID domain_id	2ahuA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	2ahuA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	2ahuB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	2ahuB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	2ahuC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	2ahuC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	2ahuD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

Domain ID domain_id	2ahuD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1080 — Glutaconate Coenzyme A-transferase
Homologous superfamily homologous superfamily	10 — Glutaconate Coenzyme A-transferase

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Unit-cell length a length_a	81.129 Å
Unit-cell length b length_b	133.308 Å
Unit-cell length c length_c	105.838 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1903
R_work r_work	0.1871
R_free r_free	0.2204

Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.

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

putative enzyme ydiF

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

2ahu__assembly_1__model_1

2ahu__assembly_1__model_1 | I(q)

2ahu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.

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

putative enzyme ydiF

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

2ahu__assembly_1__model_1

2ahu__assembly_1__model_1 | I(q)

2ahu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)