SAXSdb — 2zy4

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

L-aspartate beta-decarboxylase

Alcaligenes faecalis subsp. faecalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	PYRIDOXAL-5'-PHOSPHATE × 12 CHLORIDE ION × 12 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q93QX0_ALCFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–533； UniProt 1–533 Author chain B； PDBConstruct 1–533； UniProt 1–533 Author chain C； PDBConstruct 1–533； UniProt 1–533 Author chain D； PDBConstruct 1–533； UniProt 1–533 Author chain E； PDBConstruct 1–533； UniProt 1–533 Author chain F； PDBConstruct 1–533； UniProt 1–533

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	2zy4
Deposition date deposition_date	2009-01-13
Structure title title	dodecameric L-aspartate beta-decarboxylase
Keywords keywords	;pyridoxal 5'-phosphate, aminotransferase, 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.

2zy4__assembly_1__model_1

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

Download this curve (.dat)

2zy4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zy4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.17 Å
Rg (electron density)	54.50 Å
Total Rg	54.74 Å
Atom count	49066
Residues	6212
Excluded volume	874380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zy4__assembly_1__model_1`	dodecameric （12）	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	L-aspartate beta-decarboxylase
Molecular weight formula_weight	61173.5 kDa
EC 编号 ec_number	4.1.1.12
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	27823

MSKDYQSLAKLSPFELKDELIKIASSDGNRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAESELSYSYMTTVGVGGLAKIDGIEGRFERYIAENRDQEGVRFLGKSLSYVRDQLGLDPAAFLHEMVDGILGCNYPVPPRMLNISEKIVRQYIIREMGADAIPSESVNLFAVEGGTAAMAYIFESLKLNGLLKAGDKVAIGMPVFTPYIEIPELAQYALEEVAINADPSLNWQYPDSELDKLKDPAIKIFFCVNPSNPPSVKMDQRSLERVRNIVAEHRPDLMILTDDVYGTFADDFQSLFAICPENTLLVYSFSKYFGATGWRLGVVAAHQQNVFDLALDKLQESEKVALDHRYRSLLPDVRSLKFIDRLVADSRAVALNHTAGLSTPQQVQMALFSLFALMDEADEYKHTLKQLIRRRETTLYRELGMPPLRDENAVDYYTLIDLQDVTAKLYGEAFSEWAVKQSSTGDMLFRIADETGIVLLPGRGFGSNRPSGRASLANLNEYEYAAIGRALRKMADELYAEYSGQAQNLKLAAALEHHHHHH

Source Source

Source organism organism	Alcaligenes faecalis subsp. faecalis
NCBI taxonomy ID ncbi_taxonomy_id	32001
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	3290

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2zy4A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zy4A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2zy4B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zy4B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2zy4C01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zy4C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2zy4D01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zy4D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2zy4E01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zy4E02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2zy4F01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	2zy4F02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	110 —

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Unit-cell length a length_a	149.953 Å
Unit-cell length b length_b	217.149 Å
Unit-cell length c length_c	207.154 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1589
R_work r_work	0.1565
R_free r_free	0.2045

dodecameric L-aspartate beta-decarboxylase

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

L-aspartate beta-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

2zy4__assembly_1__model_1

2zy4__assembly_1__model_1 | I(q)

2zy4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

dodecameric L-aspartate beta-decarboxylase

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

L-aspartate beta-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

2zy4__assembly_1__model_1

2zy4__assembly_1__model_1 | I(q)

2zy4__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)