SAXSdb — 1vkp

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

AGMATINE IMINOHYDROLASE

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 1,2-ETHANEDIOL × 13 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 water × 2	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	1vkp
Deposition date deposition_date	2004-06-15
Structure title title	X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G08170, AGMATINE IMINOHYDROLASE
Keywords keywords	;structural genomics, protein structure initiative, At5g08170, POLYAMINE BIOSYNTHESIS, AGMATINE IMINOHYDROLASE, AIH, AGMATINE DEIMINASE, N-CARBAMOYLPUTRESCINE, PUTRESCINE, 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.

1vkp__assembly_1__model_1

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

Download this curve (.dat)

1vkp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vkp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.98 Å
Rg (electron density)	29.69 Å
Total Rg	30.24 Å
Atom count	5851
Residues	714
Excluded volume	103080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vkp__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 (5)

Entity 1 Entity 1 polymer

Description description	AGMATINE IMINOHYDROLASE
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	6699

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	d1vkpa_
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	d1vkpb_
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	1vkpA00
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	1vkpB00
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	19.880 Å
R factor r_factor	0.1480
R_work r_work	0.1460
R_free r_free	0.1740

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G08170, AGMATINE IMINOHYDROLASE

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

AGMATINE IMINOHYDROLASE

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

1vkp__assembly_1__model_1

1vkp__assembly_1__model_1 | I(q)

1vkp__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)

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G08170, AGMATINE IMINOHYDROLASE

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

AGMATINE IMINOHYDROLASE

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

1vkp__assembly_1__model_1

1vkp__assembly_1__model_1 | I(q)

1vkp__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)