SAXSdb — 2eja

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

Uroporphyrinogen decarboxylase

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCUP_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–338； UniProt 1–338 Author chain B； PDBConstruct 1–338； UniProt 1–338

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	2eja
Deposition date deposition_date	2007-03-16
Structure title title	Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex aeolicus
Keywords keywords	;Uroporphyrinogen Decarboxylase, Dimer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2eja__assembly_1__model_1

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

Download this curve (.dat)

2eja__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2eja__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.71 Å
Rg (electron density)	26.51 Å
Total Rg	27.57 Å
Atom count	5452
Residues	673
Excluded volume	98894 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2eja__assembly_1__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	Uroporphyrinogen decarboxylase
Molecular weight formula_weight	38729.7 kDa
EC 编号 ec_number	4.1.1.37
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	6206

MPKNDLLLRSLRGEPIGRFPVWLMRQAGRYMPEYRKIRNRVKNFLELCKNVDLATEISLLPLKILGVDAIIIFSDILVPLEPLGVKVEFVEGEGPKLSWSGKVSDLKKYDPSQNAYVYEIIKRVKEAQDEVPVIGFAGAPFTLLSYLIEGGASKDFKSTKLFMWENPKEYKRLMDILTETVLAYLKEQIKAGADVVQIFDSWVNNLSLEDYGEYVYPYVNYLISELKDFSDTPVIYFFRGSSSFIDLAVDYRADALSVDWSVDIPELFKIYDKGFQGNLEPAVLYASEEVIEEKTLGLLRRIPVKTRYVFNLGHGLAPDMELEKVKYLVDLVKSFPLT

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	751

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ejaa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.22 — UROD/MetE-like
Family Family family	c.1.22.0 — automated matches

Domain ID domain_id	d2ejab_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.22 — UROD/MetE-like
Family Family family	c.1.22.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2ejaA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	210 —

Domain ID domain_id	2ejaB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	210 —

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Unit-cell length a length_a	65.473 Å
Unit-cell length b length_b	80.403 Å
Unit-cell length c length_c	128.999 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	26.790 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2700

Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex aeolicus

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

Uroporphyrinogen 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

2eja__assembly_1__model_1

2eja__assembly_1__model_1 | I(q)

2eja__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex aeolicus

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

Uroporphyrinogen 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

2eja__assembly_1__model_1

2eja__assembly_1__model_1 | I(q)

2eja__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)