SAXSdb — 6oyy

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

Aspartate 1-decarboxylase beta chain

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	PYRAZINE-2-CARBOXYLIC ACID × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	PYRAZINE-2-CARBOXYLIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAND_MYCTU
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–24； UniProt 1–24 Author chain C； PDBConstruct 1–24； UniProt 1–24 Author chain E； PDBConstruct 1–24； UniProt 1–24 Author chain G； PDBConstruct 1–24； UniProt 1–24 Author chain I； PDBConstruct 1–24； UniProt 1–24 Author chain K； PDBConstruct 1–24； UniProt 1–24 Author chain B； PDBConstruct 1–115； UniProt 25–139 Author chain D； PDBConstruct 1–115； UniProt 25–139 Author chain F； PDBConstruct 1–115； UniProt 25–139 Author chain H； PDBConstruct 1–115； UniProt 25–139 Author chain J； PDBConstruct 1–115； UniProt 25–139 Author chain L； PDBConstruct 1–115； UniProt 25–139

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	6oyy
Deposition date deposition_date	2019-05-15
Structure title title	Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex
Keywords keywords	active, pyrazinoic acid, complex, Structural Genomics, TB Structural Genomics Consortium, TBSGC, 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.

6oyy__assembly_2__model_1

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

Download this curve (.dat)

6oyy__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6oyy__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.49 Å
Rg (electron density)	21.33 Å
Total Rg	22.11 Å
Atom count	3508
Residues	456
Excluded volume	62585 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6oyy__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6oyy__assembly_2__model_1`	octameric （8）	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 (4)

Entity 1 Entity 1 polymer

Description description	Aspartate 1-decarboxylase beta chain
Molecular weight formula_weight	2751.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,I,E,K,G
Atom count atom_count	5296

MLRTMLKSKIHRATVTCADLHYVG

Source Source

Source organism organism	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Aspartate 1-decarboxylase alpha chain
Molecular weight formula_weight	13221.8 kDa
EC 编号 ec_number	4.1.1.11
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

XVTIDADLMDAADLLEGEQVTIVDIDNGARLVTYAITGERGSGVIGINGAAAHLVHPGDLVILIAYATMDDARARTYQPRIVFVDAYNKPIDMGHDPAFVPENAGELLDPRLGVGLEHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	PYRAZINE-2-CARBOXYLIC ACID
Molecular weight formula_weight	124.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6oyyB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6oyyD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6oyyF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6oyyH00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6oyyJ00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6oyyL00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	162.282 Å
Unit-cell length b length_b	162.282 Å
Unit-cell length c length_c	62.826 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	21.760 Å
R factor r_factor	0.2016
R_work r_work	0.1993
R_free r_free	0.2467

Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex

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

Aspartate 1-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

6oyy__assembly_2__model_1

6oyy__assembly_2__model_1 | I(q)

6oyy__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Mtb aspartate decarboxylase, pyrazinoic acid complex

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

Aspartate 1-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

6oyy__assembly_2__model_1

6oyy__assembly_2__model_1 | I(q)

6oyy__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)