SAXSdb — 6p1y

▼

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	AMMONIUM ION × 4 L(+)-TARTARIC ACID × 4 water × 8	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 B； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6p1y
Deposition date deposition_date	2019-05-20
Structure title title	Crystal structure of Mtb aspartate decarboxylase mutant M117I
Keywords keywords	Structural Genomics, TB Structural Genomics Consortium, TBSGC, LYASE, POA, drug-resistance, mutant; LYASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6p1y__assembly_1__model_1

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

Download this curve (.dat)

6p1y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6p1y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.15 Å
Rg (electron density)	22.01 Å
Total Rg	22.72 Å
Atom count	3824
Residues	500
Excluded volume	68012 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6p1y__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Aspartate 1-decarboxylase beta chain
Molecular weight formula_weight	2751.3 kDa
EC 编号 ec_number	4.1.1.11
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	995

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	13203.7 kDa
EC 编号 ec_number	4.1.1.11
Mutation mutation	M117I
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XVTIDADLMDAADLLEGEQVTIVDIDNGARLVTYAITGERGSGVIGINGAAAHLVHPGDLVILIAYATMDDARARTYQPRIVFVDAYNKPIDIGHDPAFVPENAGELLDPRLGVGLEHHHHHH

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	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	nat
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	39

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6p1yB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	73.011 Å
Unit-cell length b length_b	73.011 Å
Unit-cell length c length_c	109.530 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	36.510 Å
R factor r_factor	0.1758
R_work r_work	0.1743
R_free r_free	0.2038

Crystal structure of Mtb aspartate decarboxylase mutant M117I

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

6p1y__assembly_1__model_1

6p1y__assembly_1__model_1 | I(q)

6p1y__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 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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Mtb aspartate decarboxylase mutant M117I

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

6p1y__assembly_1__model_1

6p1y__assembly_1__model_1 | I(q)

6p1y__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 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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)