1n13

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

Method: X-RAY DIFFRACTION

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

Pyruvoyl-dependent arginine decarboxylase beta chain

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	AGMATINE × 3 (4R)-2-METHYLPENTANE-2,4-DIOL × 4 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	AGMATINE × 3 (4R)-2-METHYLPENTANE-2,4-DIOL × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDAD_METJA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–52； UniProt 1–52 Author chain C； PDBConstruct 1–52； UniProt 1–52 Author chain E； PDBConstruct 1–52； UniProt 1–52 Author chain G； PDBConstruct 1–52； UniProt 1–52 Author chain I； PDBConstruct 1–52； UniProt 1–52 Author chain K； PDBConstruct 1–52； UniProt 1–52 Author chain B； PDBConstruct 1–113； UniProt 54–165 Author chain D； PDBConstruct 1–113； UniProt 54–165 Author chain F； PDBConstruct 1–113； UniProt 54–165 Author chain H； PDBConstruct 1–113； UniProt 54–165 Author chain J； PDBConstruct 1–113； UniProt 54–165 Author chain L； PDBConstruct 1–113； UniProt 54–165

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	1n13
Deposition date deposition_date	2002-10-16
Structure title title	The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii
Keywords keywords	pyruvoyl group, pyruvate, arginine decarboxylase, agmatine, arginine, 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.

1n13__assembly_1__model_1

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

Download this curve (.dat)

1n13__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1n13__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.05 Å
Rg (electron density)	21.75 Å
Total Rg	22.75 Å
Atom count	3690
Residues	480
Excluded volume	67035 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1n13__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1n13__assembly_2__model_1`	hexameric （6）	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	Pyruvoyl-dependent arginine decarboxylase beta chain
Molecular weight formula_weight	5428.1 kDa
EC 编号 ec_number	4.1.1.19
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	8260

MNAEINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRIS

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Pyruvoyl-dependent arginine decarboxylase alpha chain
Molecular weight formula_weight	12297.4 kDa
EC 编号 ec_number	4.1.1.19
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

XIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	AGMATINE
Molecular weight formula_weight	130.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	736

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1n13.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
Superfamily Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
Family Family family	d.155.1.2 — Arginine decarboxylase

Domain ID domain_id	d1n13.2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
Superfamily Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
Family Family family	d.155.1.2 — Arginine decarboxylase

Domain ID domain_id	d1n13.3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
Superfamily Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
Family Family family	d.155.1.2 — Arginine decarboxylase

Domain ID domain_id	d1n13.4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
Superfamily Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
Family Family family	d.155.1.2 — Arginine decarboxylase

Domain ID domain_id	d1n13.5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
Superfamily Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
Family Family family	d.155.1.2 — Arginine decarboxylase

Domain ID domain_id	d1n13.6
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
Superfamily Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
Family Family family	d.155.1.2 — Arginine decarboxylase

CATH v4.4 (12 domains)

Domain ID domain_id	1n13A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1n13B00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
Homologous superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

Domain ID domain_id	1n13C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1n13D00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
Homologous superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

Domain ID domain_id	1n13E00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1n13F00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
Homologous superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

Domain ID domain_id	1n13G00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1n13H00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
Homologous superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

Domain ID domain_id	1n13I00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1n13J00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
Homologous superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

Domain ID domain_id	1n13K00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1n13L00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	20 — Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
Homologous superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylase, subunit B

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Unit-cell length a length_a	56.460 Å
Unit-cell length b length_b	92.880 Å
Unit-cell length c length_c	87.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	29.160 Å
R factor r_factor	0.1915
R_work r_work	0.1915
R_free r_free	0.2150

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

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

Pyruvoyl-dependent arginine decarboxylase beta chain

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

1n13__assembly_1__model_1

1n13__assembly_1__model_1 | I(q)

1n13__assembly_1__model_1 | 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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

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

Pyruvoyl-dependent arginine decarboxylase beta chain

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

1n13__assembly_1__model_1

1n13__assembly_1__model_1 | I(q)

1n13__assembly_1__model_1 | 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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)