SAXSdb — 1pyu

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

Aspartate 1-decarboxylase beta chain

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	SULFATE ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAND_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 18–41； UniProt 1–24 Author chain C； PDBConstruct 18–41； UniProt 1–24 Author chain B； PDBConstruct 1–102； UniProt 25–126 Author chain D； PDBConstruct 1–102； UniProt 25–126

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	1pyu
Deposition date deposition_date	2003-07-09
Structure title title	Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys
Keywords keywords	Auto-processing, Aspartate Decarboxylase, pyruvoyl, 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.

1pyu__assembly_1__model_1

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

Download this curve (.dat)

1pyu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pyu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.70 Å
Rg (electron density)	21.53 Å
Total Rg	22.32 Å
Atom count	3574
Residues	470
Excluded volume	62938 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pyu__assembly_1__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	4770.6 kDa
EC 编号 ec_number	4.1.1.11
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1979

MRGSHHHHHHGLVPRGSMIRTMLQGKLHRVKVTHADLHYEG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Aspartate 1-decarboxylase alfa chain
Molecular weight formula_weight	11043.4 kDa
EC 编号 ec_number	4.1.1.11
Mutation mutation	S25C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

CCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAAERGSRIISVNGAAAHCASVGDIVIIASFVTMPDEEARTWRPNVAYFEGDNEMKRTAKAIPVQVA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	180

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1pyu.1
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.1 — Pyruvoyl dependent aspartate decarboxylase, ADC

Domain ID domain_id	d1pyu.2
Class class	b — All beta proteins
Fold Fold fold	b.52 — Double psi beta-barrel
Superfamily Superfamily superfamily	b.52.2 — ADC-like
Family Family family	b.52.2.1 — Pyruvoyl dependent aspartate decarboxylase, ADC

CATH v4.4 (2 domains)

Domain ID domain_id	1pyuB00
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	1pyuD00
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	70.787 Å
Unit-cell length b length_b	70.787 Å
Unit-cell length c length_c	217.121 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1738
R_work r_work	0.1726
R_free r_free	0.1961

Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys

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

1pyu__assembly_1__model_1

1pyu__assembly_1__model_1 | I(q)

1pyu__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)

Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys

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

1pyu__assembly_1__model_1

1pyu__assembly_1__model_1 | I(q)

1pyu__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)