1n2m

The S53A Proenzyme Structure of Methanococcus jannaschii.

Method: X-RAY DIFFRACTION

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

Pyruvoyl-dependent arginine decarboxylase

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	(4R)-2-METHYLPENTANE-2,4-DIOL × 4 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	(4R)-2-METHYLPENTANE-2,4-DIOL × 4 water × 3	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
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 1–165 Author chain B； PDBConstruct 1–165； UniProt 1–165 Author chain C； PDBConstruct 1–165； UniProt 1–165 Author chain D； PDBConstruct 1–165； UniProt 1–165 Author chain E； PDBConstruct 1–165； UniProt 1–165 Author chain F； PDBConstruct 1–165； UniProt 1–165

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	1n2m
Deposition date deposition_date	2002-10-23
Structure title title	The S53A Proenzyme Structure of Methanococcus jannaschii.
Keywords keywords	pyruvoyl group, pyruvate, agmatine, arginine decarboxylase, 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.

1n2m__assembly_2__model_1

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

Download this curve (.dat)

1n2m__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1n2m__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.71 Å
Rg (electron density)	21.41 Å
Total Rg	22.39 Å
Atom count	3544
Residues	469
Excluded volume	64431 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1n2m__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1n2m__assembly_2__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Pyruvoyl-dependent arginine decarboxylase
Molecular weight formula_weight	17708.6 kDa
EC 编号 ec_number	4.1.1.19
Mutation mutation	S53A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7837

MNAEINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISAIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK

Source Source

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

Entity 2 Entity 2 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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	498

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1n2ma_
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	d1n2mb_
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	d1n2mc_
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	d1n2md_
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	d1n2me_
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	d1n2mf_
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 (6 domains)

Domain ID domain_id	1n2mA00
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	1n2mB00
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	1n2mC00
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	1n2mD00
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	1n2mE00
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	1n2mF00
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	56.260 Å
Unit-cell length b length_b	91.310 Å
Unit-cell length c length_c	86.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.72 °
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	1.900 Å
Low-resolution limit resolution_low	28.690 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2210

The S53A Proenzyme Structure of Methanococcus jannaschii.

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

Pyruvoyl-dependent arginine 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

1n2m__assembly_2__model_1

1n2m__assembly_2__model_1 | I(q)

1n2m__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

The S53A Proenzyme Structure of Methanococcus jannaschii.

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

Pyruvoyl-dependent arginine 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

1n2m__assembly_2__model_1

1n2m__assembly_2__model_1 | I(q)

1n2m__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)