2idb

Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.

Method: X-RAY DIFFRACTION

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

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	PENTAETHYLENE GLYCOL × 6 1,2-ETHANEDIOL × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBID_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–497； UniProt 1–497 Author chain B； PDBConstruct 1–497； UniProt 1–497 Author chain C； PDBConstruct 1–497； UniProt 1–497

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	2idb
Deposition date deposition_date	2006-09-14
Structure title title	Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.
Keywords keywords	alpha-beta protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

2idb__assembly_1__model_1

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

Download this curve (.dat)

2idb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2idb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.89 Å
Rg (electron density)	45.25 Å
Total Rg	45.44 Å
Atom count	21928
Residues	2706
Excluded volume	392550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2idb__assembly_1__model_1`	hexameric （6）	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	3-octaprenyl-4-hydroxybenzoate carboxy-lyase
Molecular weight formula_weight	57346.3 kDa
EC 编号 ec_number	4.1.1.-
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	11118

MDAMKYNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKEPEPPKGFRDLFDKLPQFKQVLNMPTKRLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIFNNGKSALEHHHHHH

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2idba1
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.3 — UbiD middle domain-like

Domain ID domain_id	d2idba2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.333 — UbiD C-terminal domain-like
Superfamily Superfamily superfamily	d.333.1 — UbiD C-terminal domain-like
Family Family family	d.333.1.1 — UbiD C-terminal domain-like

Domain ID domain_id	d2idbb1
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.3 — UbiD middle domain-like

Domain ID domain_id	d2idbb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.333 — UbiD C-terminal domain-like
Superfamily Superfamily superfamily	d.333.1 — UbiD C-terminal domain-like
Family Family family	d.333.1.1 — UbiD C-terminal domain-like

Domain ID domain_id	d2idbc1
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.3 — UbiD middle domain-like

Domain ID domain_id	d2idbc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.333 — UbiD C-terminal domain-like
Superfamily Superfamily superfamily	d.333.1 — UbiD C-terminal domain-like
Family Family family	d.333.1.1 — UbiD C-terminal domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	2idbA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1670 — UbiD C-terminal domain-like
Homologous superfamily homologous superfamily	10 — UbiD C-terminal domain-like

Domain ID domain_id	2idbA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	570 — Single helix bin

Domain ID domain_id	2idbB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1670 — UbiD C-terminal domain-like
Homologous superfamily homologous superfamily	10 — UbiD C-terminal domain-like

Domain ID domain_id	2idbB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	570 — Single helix bin

Domain ID domain_id	2idbC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1670 — UbiD C-terminal domain-like
Homologous superfamily homologous superfamily	10 — UbiD C-terminal domain-like

Domain ID domain_id	2idbC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	570 — Single helix bin

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Unit-cell length a length_a	194.295 Å
Unit-cell length b length_b	194.295 Å
Unit-cell length c length_c	106.051 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	40.200 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2650

Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.

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

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

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

2idb__assembly_1__model_1

2idb__assembly_1__model_1 | I(q)

2idb__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.

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

3-octaprenyl-4-hydroxybenzoate carboxy-lyase

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

2idb__assembly_1__model_1

2idb__assembly_1__model_1 | I(q)

2idb__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)