SAXSdb — 3cmb

▼

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

Acetoacetate decarboxylase

Methanoculleus marisnigri JR1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SODIUM ION × 12 CHLORIDE ION × 4 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 2 DI(HYDROXYETHYL)ETHER × 9 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3CUL0_METMJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–283； UniProt 1–264 Author chain B； PDBConstruct 20–283； UniProt 1–264 Author chain C； PDBConstruct 20–283； UniProt 1–264 Author chain D； PDBConstruct 20–283； UniProt 1–264

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	3cmb
Deposition date deposition_date	2008-03-21
Structure title title	Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution
Keywords keywords	;YP_001047042.1, Acetoacetate decarboxylase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, LYASE ;; 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.

3cmb__assembly_1__model_1

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

Download this curve (.dat)

3cmb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cmb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.94 Å
Rg (electron density)	29.65 Å
Total Rg	30.45 Å
Atom count	8460
Residues	1034
Excluded volume	152570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cmb__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Acetoacetate decarboxylase
Molecular weight formula_weight	32180.2 kDa
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	10029

MGSDKIHHHHHHENLYFQGMFRPQDDFTYLMPVHFGGGKFDPETLVTQKATALSLSFETERDLLENYIPEGFELLAPEVQVAFNKFTEINWLHGGQYNLINVAAPVRFHGKKDELDGAYTLVVWENKTAPILGGREQTGIPKIYADIEDLHIVRPHFATTVSYEGNTFLNMDFEATGSITGRDLDALKSQFLTMNTLGWRYIPKVGAPGAELSQFVLYPQGMEVETAEVGKGSLKWTELTPMQSPAQYYIVNSLASLPIKRVTQAVLVEGRAILRAMGARVIE

Source Source

Source organism organism	Methanoculleus marisnigri JR1
NCBI taxonomy ID ncbi_taxonomy_id	368407
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	12

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	4

Entity 4 Entity 4 non-polymer

Description description	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
Molecular weight formula_weight	326.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 6 Entity 6 non-polymer

Description description	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
Molecular weight formula_weight	370.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1360

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3cmba1
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	d3cmba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3cmbb2
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	d3cmbb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3cmbc2
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	d3cmbc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3cmbd2
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	d3cmbd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	3cmbA00
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	3cmbB00
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	3cmbC00
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	3cmbD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	400 — Acetoacetate decarboxylase-like
Homologous superfamily homologous superfamily	10 — Acetoacetate decarboxylase-like

▶

Unit-cell length a length_a	129.340 Å
Unit-cell length b length_b	136.710 Å
Unit-cell length c length_c	168.120 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	32

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	29.386 Å
R factor r_factor	0.2290
R_work r_work	0.2280
R_free r_free	0.2590

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution

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

Acetoacetate 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

3cmb__assembly_1__model_1

3cmb__assembly_1__model_1 | I(q)

3cmb__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution

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

Acetoacetate 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

3cmb__assembly_1__model_1

3cmb__assembly_1__model_1 | I(q)

3cmb__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)