2qqc

E109Q mutant 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 subunit beta

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 (4S)-2-METHYL-2,4-PENTANEDIOL × 3 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	AGMATINE × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 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 2–53； UniProt 1–52 Author chain C； PDBConstruct 2–53； UniProt 1–52 Author chain E； PDBConstruct 2–53； UniProt 1–52 Author chain G； PDBConstruct 2–53； UniProt 1–52 Author chain I； PDBConstruct 2–53； UniProt 1–52 Author chain K； PDBConstruct 2–53； UniProt 1–52 Author chain B； PDBConstruct 2–113； UniProt 54–165 Author chain D； PDBConstruct 2–113； UniProt 54–165 Author chain F； PDBConstruct 2–113； UniProt 54–165 Author chain H； PDBConstruct 2–113； UniProt 54–165 Author chain J； PDBConstruct 2–113； UniProt 54–165 Author chain L； PDBConstruct 2–113； 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	2qqc
Deposition date deposition_date	2007-07-26
Structure title title	E109Q mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii
Keywords keywords	arginine decarboxylase, pyruvoyl, decarboxylation, autoprocessing, serinolysis, Lyase, Pyruvate; 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.

2qqc__assembly_2__model_1

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

Download this curve (.dat)

2qqc__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qqc__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.83 Å
Rg (electron density)	21.57 Å
Total Rg	22.52 Å
Atom count	3458
Residues	456
Excluded volume	62759 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qqc__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qqc__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 subunit beta
Molecular weight formula_weight	5566.3 kDa
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	7630

HMNAEINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRIS

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 subunit alpha
Molecular weight formula_weight	12296.4 kDa
Mutation mutation	E109Q
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

XIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMQYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK

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	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	501

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2qqcA00
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	2qqcB00
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	2qqcC00
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	2qqcD00
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	2qqcE00
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	2qqcF00
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	2qqcG00
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	2qqcH00
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	2qqcI00
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	2qqcJ00
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	2qqcK00
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	2qqcL00
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	58.108 Å
Unit-cell length b length_b	92.810 Å
Unit-cell length c length_c	85.707 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.11 °
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	2.000 Å
Low-resolution limit resolution_low	44.030 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2370

E109Q mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

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

Pyruvoyl-dependent arginine decarboxylase subunit beta

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

2qqc__assembly_2__model_1

2qqc__assembly_2__model_1 | I(q)

2qqc__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 (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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

E109Q mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

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

Pyruvoyl-dependent arginine decarboxylase subunit beta

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

2qqc__assembly_2__model_1

2qqc__assembly_2__model_1 | I(q)

2qqc__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 (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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)