SAXSdb — 2p3e

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

Diaminopimelate 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	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCDA_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 1–420 Author chain B； PDBConstruct 1–420； UniProt 1–420

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	2p3e
Deposition date deposition_date	2007-03-08
Structure title title	Crystal structure of AQ1208 from Aquifex aeolicus
Keywords keywords	;AQ1208, Aquifex aeolicus, SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS, RIKEN SPring-8 Center, RIKEN Genomic Sciences Center, Department of Biological Sciences Osaka University, Department of Biophysics and Biochemistry University of Tokyo, PSI, Protein Structure Initiative, SECSG, 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.

2p3e__assembly_1__model_1

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

Download this curve (.dat)

2p3e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p3e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.67 Å
Rg (electron density)	27.74 Å
Total Rg	28.57 Å
Atom count	6299
Residues	801
Excluded volume	113290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p3e__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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2p3eA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

Domain ID domain_id	2p3eA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	10 — Alanine racemase

Domain ID domain_id	2p3eB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	37 — Lyase, Ornithine Decarboxylase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Lyase, Ornithine Decarboxylase; Chain A, domain 1

Domain ID domain_id	2p3eB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	10 — Alanine racemase

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Unit-cell length a length_a	75.515 Å
Unit-cell length b length_b	87.675 Å
Unit-cell length c length_c	152.581 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	1.990 Å
Low-resolution limit resolution_low	8.740 Å
R factor r_factor	0.1865
R_work r_work	0.1848
R_free r_free	0.2179

Description description	Diaminopimelate decarboxylase
Molecular weight formula_weight	47026.9 kDa
EC 编号 ec_number	4.1.1.20
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6860

Crystal structure of AQ1208 from Aquifex aeolicus

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

Diaminopimelate 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

2p3e__assembly_1__model_1

2p3e__assembly_1__model_1 | I(q)

2p3e__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	561

Crystal structure of AQ1208 from Aquifex aeolicus

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

Diaminopimelate 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

2p3e__assembly_1__model_1

2p3e__assembly_1__model_1 | I(q)

2p3e__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)