SAXSdb — 3fdd

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

L-aspartate-beta-decarboxylase

Pseudomonas dacunhae ATCC 21192

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 ACETATE ION × 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	Q845W8_COMTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； 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	3fdd
Deposition date deposition_date	2008-11-25
Structure title title	The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme
Keywords keywords	;L-aspartate-beta-decarboxylase, Aspartate 4-decarboxylase, L-aspartate 4-carboxy-lyase, pyridoxal-5'-phosphate, PLP, aspD, dodecamer, ABDC, 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.

3fdd__assembly_1__model_1

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

Download this curve (.dat)

3fdd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fdd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.83 Å
Rg (electron density)	54.16 Å
Total Rg	54.42 Å
Atom count	47616
Residues	6024
Excluded volume	847910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fdd__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 (5)

Entity 1 Entity 1 polymer

Description description	L-aspartate-beta-decarboxylase
Molecular weight formula_weight	59581.7 kDa
EC 编号 ec_number	4.1.1.12
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	4180

MSKDYQSLANLSPFELKDELIKIASGDGNRLMLNAGRGNPNFLATTPRRAFFRLGLFAAAESELSYSYMNTVGVGGLAKIEGIEGRFERYIAENRDQEGVRFLGKSLSYVRDQLGLDPAAFLHEMVDGILGCNYPVPPRMLNISEKIVRQYIIREMGADAIPSESVNLFAVEGGTAAMAYIFESMKVNGLLKAGDKVAIGMPVFTPYIEIPELAQYALEEVAINADPALNWQYPDSELDKLKDPAIKIFFCVNPSNPPSVKMDERSLERVRKIVAEHRPDLMILTDDVYGTFADGFQSLFAICPANTLLVYSFSKYFGATGWRLGVVAAHKENIFDLALGRLPESEKTALDDRYRSLLPDVRSLKFLDRLVADSRAVALNHTAGLSTPQQVQMTLFSLFALMDESDQYKHTLKQLIRRREATLYRELGTPPQRDENAVDYYTLIDLQDVTSKLYGEAFSKWAVKQSSTGDMLFRIADETGIVLLPGRGFGSDRPSGRASLANLNEYEYAAIGRALRQMADELYAQYTQQGNKR

Source Source

Source organism organism	Pseudomonas dacunhae ATCC 21192
NCBI taxonomy ID ncbi_taxonomy_id	207291
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	1

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
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	212

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3fddA03
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

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Unit-cell length a length_a	150.453 Å
Unit-cell length b length_b	150.453 Å
Unit-cell length c length_c	150.453 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	106.600 Å
R factor r_factor	0.1700
R_work r_work	0.1680
R_free r_free	0.2120

The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme

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

3fdd__assembly_1__model_1

3fdd__assembly_1__model_1 | I(q)

3fdd__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 non-polymer

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)

The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme

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

3fdd__assembly_1__model_1

3fdd__assembly_1__model_1 | I(q)

3fdd__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 non-polymer

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)