SAXSdb — 2qeu

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

Putative carboxymuconolactone decarboxylase

Burkholderia xenovorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ACETATE ION × 14 CITRIC ACID × 6 GLYCEROL × 8 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q13HH1_BURXL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–141； UniProt 1–140 Author chain B； PDBConstruct 2–141； UniProt 1–140 Author chain C； PDBConstruct 2–141； UniProt 1–140

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	2qeu
Deposition date deposition_date	2007-06-26
Structure title title	Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution
Keywords keywords	;YP_555818.1, Putative carboxymuconolactone decarboxylase, Carboxymuconolactone decarboxylase family, 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.

2qeu__assembly_1__model_1

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

Download this curve (.dat)

2qeu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qeu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.02 Å
Rg (electron density)	25.76 Å
Total Rg	26.42 Å
Atom count	6232
Residues	764
Excluded volume	112380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qeu__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 (5)

Entity 1 Entity 1 polymer

Description description	Putative carboxymuconolactone decarboxylase
Molecular weight formula_weight	15732.1 kDa
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	3764

GMDQESNATSQDILKQHAAHYESDMGGLPEALVQLAEYAPETFDAYSRMRTTMLKSEADGAKLPLKYKHLILVVLDAIRDEPIGIVNHTRAAMNAGLSVDELIEGILLGIIVYGMPAWGKTGRKAVTFAVEFEKELAGKRT

Source Source

Source organism organism	Burkholderia xenovorans
NCBI taxonomy ID ncbi_taxonomy_id	266265
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	410

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2qeuA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2qeuB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

Domain ID domain_id	2qeuC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1290 — AhpD-like
Homologous superfamily homologous superfamily	10 — AhpD-like

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Unit-cell length a length_a	71.173 Å
Unit-cell length b length_b	71.173 Å
Unit-cell length c length_c	325.501 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	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	29.761 Å
R factor r_factor	0.1540
R_work r_work	0.1520
R_free r_free	0.1800

Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution

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

Putative carboxymuconolactone decarboxylase

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

2qeu__assembly_1__model_1

2qeu__assembly_1__model_1 | I(q)

2qeu__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of putative carboxymuconolactone decarboxylase (YP_555818.1) from Burkholderia xenovorans LB400 at 1.65 A resolution

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

Putative carboxymuconolactone decarboxylase

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

2qeu__assembly_1__model_1

2qeu__assembly_1__model_1 | I(q)

2qeu__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)