SAXSdb — 1ko0

▼

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

Diaminopimelate decarboxylase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PYRIDOXAL-5'-PHOSPHATE × 2 LYSINE × 2 D-LYSINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCDA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ko0
Deposition date deposition_date	2001-12-19
Structure title title	Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase
Keywords keywords	;pyridoxal-5'-phosphate, diaminopimelate, lysine, PLP, TIM-barrel, LYASE ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1ko0__assembly_1__model_1

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

Download this curve (.dat)

1ko0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ko0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.12 Å
Rg (electron density)	27.19 Å
Total Rg	27.87 Å
Atom count	6538
Residues	838
Excluded volume	115220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ko0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Diaminopimelate decarboxylase
Molecular weight formula_weight	46920.8 kDa
EC 编号 ec_number	4.1.1.20
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3693

MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELLHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	D-LYSINE
Molecular weight formula_weight	146.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	384

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ko0a1
Class class	b — All beta proteins
Fold Fold fold	b.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamily	b.49.2 — Alanine racemase C-terminal domain-like
Family Family family	b.49.2.3 — Eukaryotic ODC-like

Domain ID domain_id	d1ko0a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.6 — PLP-binding barrel
Family Family family	c.1.6.1 — Alanine racemase-like, N-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1ko0A01
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	1ko0A02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	10 — Alanine racemase

▶

Unit-cell length a length_a	98.997 Å
Unit-cell length b length_b	98.997 Å
Unit-cell length c length_c	176.966 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	12

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1810
R_free r_free	0.2460

Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase

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

1ko0__assembly_1__model_1

1ko0__assembly_1__model_1 | I(q)

1ko0__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of a D,L-lysine complex of diaminopimelate decarboxylase

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

1ko0__assembly_1__model_1

1ko0__assembly_1__model_1 | I(q)

1ko0__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)