2aal

Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities

Method: X-RAY DIFFRACTION

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

Malonate semialdehyde decarboxylase

Pseudomonas pavonaceae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MALONATE ION × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	MALONATE ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9EV83_PSEPV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 2–130 Author chain B； PDBConstruct 1–129； UniProt 2–130 Author chain C； PDBConstruct 1–129； UniProt 2–130 Author chain D； PDBConstruct 1–129； UniProt 2–130 Author chain E； PDBConstruct 1–129； UniProt 2–130 Author chain F； PDBConstruct 1–129； UniProt 2–130

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	2aal
Deposition date deposition_date	2005-07-13
Structure title title	Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities
Keywords keywords	tautomerase superfamily; beta-alpha-beta; homotrimeric, 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.

2aal__assembly_1__model_1

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

Download this curve (.dat)

2aal__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2aal__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.01 Å
Rg (electron density)	19.53 Å
Total Rg	20.43 Å
Atom count	2998
Residues	388
Excluded volume	53051 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2aal__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2aal__assembly_2__model_1`	trimeric （3）	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	Malonate semialdehyde decarboxylase
Molecular weight formula_weight	14181.0 kDa
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	7105

PLLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLVG

Source Source

Source organism organism	Pseudomonas pavonaceae
NCBI taxonomy ID ncbi_taxonomy_id	47881
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	956

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2aala1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.6 — MSAD-like

Domain ID domain_id	d2aalb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.6 — MSAD-like

Domain ID domain_id	d2aalb3
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	d2aalc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.6 — MSAD-like

Domain ID domain_id	d2aald_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.6 — MSAD-like

Domain ID domain_id	d2aale_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.6 — MSAD-like

Domain ID domain_id	d2aalf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.6 — MSAD-like

CATH v4.4 (6 domains)

Domain ID domain_id	2aalA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2aalB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2aalC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2aalD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2aalE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	2aalF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

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Unit-cell length a length_a	51.889 Å
Unit-cell length b length_b	51.889 Å
Unit-cell length c length_c	219.083 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	18

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	72.550 Å
R factor r_factor	0.1864
R_work r_work	0.1837
R_free r_free	0.2387

Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities

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

Malonate semialdehyde 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

2aal__assembly_1__model_1

2aal__assembly_1__model_1 | I(q)

2aal__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) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities

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

Malonate semialdehyde 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

2aal__assembly_1__model_1

2aal__assembly_1__model_1 | I(q)

2aal__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) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)