2aci

Structure of D166A arginine deiminase

Method: X-RAY DIFFRACTION

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

Arginine deiminase

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	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	ARCA_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–418； UniProt 0–417 Author chain B； PDBConstruct 1–418； UniProt 0–417 Author chain C； PDBConstruct 1–418； UniProt 0–417 Author chain D； PDBConstruct 1–418； UniProt 0–417

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	2aci
Deposition date deposition_date	2005-07-18
Structure title title	Structure of D166A arginine deiminase
Keywords keywords	arginine degradation pathway, L-arginine deiminase, catalytic mechanism, HYDROLASE; HYDROLASE
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.

2aci__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2aci__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2aci__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.61 Å
Rg (electron density)	28.83 Å
Total Rg	29.59 Å
Atom count	6313
Residues	808
Excluded volume	112440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2aci__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2aci__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2aci__assembly_3__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)

Entity 1 Entity 1 polymer

Description description	Arginine deiminase
Molecular weight formula_weight	46446.9 kDa
EC 编号 ec_number	3.5.3.6
Mutation mutation	D166A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12953

MSTEKTKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRATTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPIDY

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	300

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2acia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.4 — Arginine deiminase

Domain ID domain_id	d2acib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.4 — Arginine deiminase

Domain ID domain_id	d2acic_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.4 — Arginine deiminase

Domain ID domain_id	d2acid_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.4 — Arginine deiminase

CATH v4.4 (8 domains)

Domain ID domain_id	2aciA01
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

Domain ID domain_id	2aciA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3930 — Pentein
Homologous superfamily homologous superfamily	10 — Arginine deiminase

Domain ID domain_id	2aciB01
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

Domain ID domain_id	2aciB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3930 — Pentein
Homologous superfamily homologous superfamily	10 — Arginine deiminase

Domain ID domain_id	2aciC01
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

Domain ID domain_id	2aciC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3930 — Pentein
Homologous superfamily homologous superfamily	10 — Arginine deiminase

Domain ID domain_id	2aciD01
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

Domain ID domain_id	2aciD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3930 — Pentein
Homologous superfamily homologous superfamily	10 — Arginine deiminase

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Unit-cell length a length_a	91.200 Å
Unit-cell length b length_b	123.900 Å
Unit-cell length c length_c	150.000 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1980
R_free r_free	0.2720

Structure of D166A arginine deiminase

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

Arginine deiminase

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

2aci__assembly_2__model_1

2aci__assembly_2__model_1 | I(q)

2aci__assembly_2__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of D166A arginine deiminase

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

Arginine deiminase

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

2aci__assembly_2__model_1

2aci__assembly_2__model_1 | I(q)

2aci__assembly_2__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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)