SAXSdb — 3c8w

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

Acetoacetate decarboxylase ADC

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	CITRIC ACID × 12 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZXQ9_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–255； UniProt 1–254 Author chain B； PDBConstruct 2–255； UniProt 1–254 Author chain C； PDBConstruct 2–255； UniProt 1–254 Author chain D； PDBConstruct 2–255； UniProt 1–254

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	3c8w
Deposition date deposition_date	2008-02-13
Structure title title	Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution
Keywords keywords	;YP_094708.1, acetoacetate decarboxylase (ADC), Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

3c8w__assembly_1__model_1

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

Download this curve (.dat)

3c8w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c8w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.81 Å
Rg (electron density)	41.95 Å
Total Rg	42.45 Å
Atom count	23496
Residues	2922
Excluded volume	425450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c8w__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 (3)

Entity 1 Entity 1 polymer

Description description	Acetoacetate decarboxylase ADC
Molecular weight formula_weight	28791.3 kDa
EC 编号 ec_number	4.1.1.4
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8626

GMDKYLSANSLEGVIDNEFSMPAPRWLNTYPAGPYRFINREFFIIAYETDPDLLQAILPPDMELLEPVVKFEFIRMPDSTGFGDYTESGQVVPVRYKGEEGGFTISMFLDCHAPIAGGREIWGFPKKLAKPKLFVEEDTLIGILKYGSIDIAIATMGYKHRPLDAEKVLESVKKPVFLLKNIPNVDGTPLVNQLTKTYLTDITVKGAWTGPGSLELHPHALAPISNLYIKKIVSVSHFITDLTLPYGKVVADYLA

Source Source

Source organism organism	Legionella pneumophila subsp. pneumophila str. Philadelphia 1
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	711

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3c8wa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.347 — Acetoacetate decarboxylase-like
Superfamily Superfamily superfamily	d.347.1 — Acetoacetate decarboxylase-like
Family Family family	d.347.1.1 — Acetoacetate decarboxylase-like

Domain ID domain_id	d3c8wb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.347 — Acetoacetate decarboxylase-like
Superfamily Superfamily superfamily	d.347.1 — Acetoacetate decarboxylase-like
Family Family family	d.347.1.1 — Acetoacetate decarboxylase-like

Domain ID domain_id	d3c8wc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.347 — Acetoacetate decarboxylase-like
Superfamily Superfamily superfamily	d.347.1 — Acetoacetate decarboxylase-like
Family Family family	d.347.1.1 — Acetoacetate decarboxylase-like

Domain ID domain_id	d3c8wd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.347 — Acetoacetate decarboxylase-like
Superfamily Superfamily superfamily	d.347.1 — Acetoacetate decarboxylase-like
Family Family family	d.347.1.1 — Acetoacetate decarboxylase-like

CATH v4.4 (4 domains)

Domain ID domain_id	3c8wA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	400 — Acetoacetate decarboxylase-like
Homologous superfamily homologous superfamily	10 — Acetoacetate decarboxylase-like

Domain ID domain_id	3c8wB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	400 — Acetoacetate decarboxylase-like
Homologous superfamily homologous superfamily	10 — Acetoacetate decarboxylase-like

Domain ID domain_id	3c8wC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	400 — Acetoacetate decarboxylase-like
Homologous superfamily homologous superfamily	10 — Acetoacetate decarboxylase-like

Domain ID domain_id	3c8wD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	400 — Acetoacetate decarboxylase-like
Homologous superfamily homologous superfamily	10 — Acetoacetate decarboxylase-like

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Unit-cell length a length_a	104.100 Å
Unit-cell length b length_b	104.100 Å
Unit-cell length c length_c	189.640 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 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	29.683 Å
R factor r_factor	0.1950
R_work r_work	0.1930
R_free r_free	0.2280

Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution

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

Acetoacetate decarboxylase ADC

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

3c8w__assembly_1__model_1

3c8w__assembly_1__model_1 | I(q)

3c8w__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution

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

Acetoacetate decarboxylase ADC

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

3c8w__assembly_1__model_1

3c8w__assembly_1__model_1 | I(q)

3c8w__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)