SAXSdb — 2q3u

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

Agmatine deiminase

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 1,2-ETHANEDIOL × 7 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 1,2-ETHANEDIOL × 6 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGUA_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–383； UniProt 1–383 Author chain B； PDBConstruct 1–383； UniProt 1–383

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	2q3u
Deposition date deposition_date	2007-05-30
Structure title title	Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase
Keywords keywords	;Ensemble Refinement, Refinement Methodology Development, At5g08170, POLYAMINE BIOSYNTHESIS, AGMATINE IMINOHYDROLASE, AIH, AGMATINE DEIMINASE, N-CARBAMOYLPUTRESCINE, PUTRESCINE, Structural Genomics, Protein Structure Initiative, PSI, Center for Eukaryotic Structural Genomics, CESG, 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.

2q3u__assembly_2__model_7

Assembly 2 · Model 7 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2q3u__assembly_2__model_7 | I(q)

100 plotted points; both axes use logarithmic scales.

2q3u__assembly_2__model_7 | P(r) · Pending

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

Rg（Guinier）	20.23 Å
Rg (electron density)	19.15 Å
Total Rg	20.03 Å
Atom count	2907
Residues	356
Excluded volume	51213 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2q3u__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2q3u__assembly_1__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2q3u__assembly_1__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2q3u__assembly_1__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2q3u__assembly_1__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2q3u__assembly_1__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2q3u__assembly_1__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2q3u__assembly_1__model_8`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2q3u__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	2	`2q3u__assembly_2__model_2`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	3	`2q3u__assembly_2__model_3`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	4	`2q3u__assembly_2__model_4`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	5	`2q3u__assembly_2__model_5`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	6	`2q3u__assembly_2__model_6`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	7	`2q3u__assembly_2__model_7`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	8	`2q3u__assembly_2__model_8`	monomeric （1）	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	Agmatine deiminase
Molecular weight formula_weight	43521.4 kDa
EC 编号 ec_number	3.5.3.12
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	53040

MEESRESPAEHGYYMPAEWDSHAQTWIGWPERQDNWRHNALPAQRVFAGVAKAISKFEPVTVCASPAQWENARKQLPEDIRVVEMSMNDSWFRDSGPTFIVRKRPVKLSSLNRNIAGIDWNFNAWGGANDGCYNDWSHDLLVSRKILALERIPRFQHSMILEGGSIHVDGEGTCLVTEECLLNKNRNPHMSKEQIEEELKKYLGVQSFIWLPRGLYGDEDTNGHIDNMCCFARPGVVLLSWTDDETDPQYERSVEALSVLSNSIDARGRKIQVIKLYIPEPLYMTEEESSGITQDGEAIPRLAGTRLAASYVNFYIANGGIIAPQFGDPIRDKEAIRVLSDTFPHHSVVGIENAREIVLAGGNIHCITQQQPAEPTSVAENGH

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	3[N-MORPHOLINO]PROPANE SULFONIC ACID
Molecular weight formula_weight	209.3 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	779

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2q3ua_
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.126.1.6 — Porphyromonas-type peptidylarginine deiminase

Domain ID domain_id	d2q3ub_
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.126.1.6 — Porphyromonas-type peptidylarginine deiminase

CATH v4.4 (2 domains)

Domain ID domain_id	2q3uA00
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	2q3uB00
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

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Unit-cell length a length_a	58.020 Å
Unit-cell length b length_b	115.813 Å
Unit-cell length c length_c	66.634 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.530 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.1350
R_work r_work	0.1350
R_free r_free	0.1710

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase

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

Agmatine 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

2q3u__assembly_2__model_7

2q3u__assembly_2__model_7 | I(q)

2q3u__assembly_2__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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)

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase

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

Agmatine 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

2q3u__assembly_2__model_7

2q3u__assembly_2__model_7 | I(q)

2q3u__assembly_2__model_7 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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)