3fa3

Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form

Method: X-RAY DIFFRACTION

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

2,3-dimethylmalate lyase

Aspergillus niger

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 2,2-difluoro-3,3-dihydroxybutanedioic acid × 4 GLYCEROL × 2 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 2,2-difluoro-3,3-dihydroxybutanedioic acid × 4 GLYCEROL × 2 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 2,2-difluoro-3,3-dihydroxybutanedioic acid × 3 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 2,2-difluoro-3,3-dihydroxybutanedioic acid × 3 GLYCEROL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2L887_ASPNG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–302； UniProt 2–303 Author chain B； PDBConstruct 1–302； UniProt 2–303 Author chain C； PDBConstruct 1–302； UniProt 2–303 Author chain D； PDBConstruct 1–302； UniProt 2–303 Author chain E； PDBConstruct 1–302； UniProt 2–303 Author chain F； PDBConstruct 1–302； UniProt 2–303 Author chain G； PDBConstruct 1–302； UniProt 2–303 Author chain H； PDBConstruct 1–302； UniProt 2–303 Author chain I； PDBConstruct 1–302； UniProt 2–303 Author chain J； PDBConstruct 1–302； UniProt 2–303 Author chain K； PDBConstruct 1–302； UniProt 2–303 Author chain L； PDBConstruct 1–302； UniProt 2–303 Author chain M； PDBConstruct 1–302； UniProt 2–303 Author chain N； PDBConstruct 1–302； UniProt 2–303 Author chain O； PDBConstruct 1–302； UniProt 2–303 Author chain P； PDBConstruct 1–302； UniProt 2–303

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	3fa3
Deposition date deposition_date	2008-11-14
Structure title title	Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form
Keywords keywords	alpha/beta barrel, HELIX SWAPPING, 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.

3fa3__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fa3__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fa3__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.25 Å
Rg (electron density)	29.33 Å
Total Rg	29.97 Å
Atom count	8972
Residues	1204
Excluded volume	158890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fa3__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fa3__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fa3__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3fa3__assembly_4__model_1`	tetrameric （4）	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	2,3-dimethylmalate lyase
Molecular weight formula_weight	32020.5 kDa
EC 编号 ec_number	4.1.3.32
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	36360

PMVTAATSLRRALENPDSFIVAPGVYDGLSARVALSAGFDALYMTGAGTAASVHGQADLGICTLNDMRANAEMISNISPSTPVIADADTGYGGPIMVARTTEQYSRSGVAAFHIEDQVQTKRCGHLAGKILVDTDTYVTRIRAAVQARQRIGSDIVVIARTDSLQTHGYEESVARLRAARDAGADVGFLEGITSREMARQVIQDLAGWPLLLNMVEHGATPSISAAEAKEMGFRIIIFPFAALGPAVAAMREAMEKLKRDGIPGLDKEMTPQMLFRVCGLDESMKVDAQAGGAAFDGGVDLK

Source Source

Source organism organism	Aspergillus niger
NCBI taxonomy ID ncbi_taxonomy_id	5061
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	2,2-difluoro-3,3-dihydroxybutanedioic acid
Molecular weight formula_weight	186.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	704

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3fa3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3k_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3l_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3m_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3n_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3o_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

Domain ID domain_id	d3fa3p_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.12 — Phosphoenolpyruvate/pyruvate domain
Family Family family	c.1.12.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id	3fa3A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3C00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3D00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3E00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3F00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3G00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3H00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3I00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3J00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3K00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3L00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3M00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3N00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3O00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

Domain ID domain_id	3fa3P00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	60 — Phosphoenolpyruvate-binding domains

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Unit-cell length a length_a	160.570 Å
Unit-cell length b length_b	160.570 Å
Unit-cell length c length_c	161.410 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	48

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1930
R_work r_work	0.1900
R_free r_free	0.2550

Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form

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

2,3-dimethylmalate lyase

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

3fa3__assembly_2__model_1

3fa3__assembly_2__model_1 | I(q)

3fa3__assembly_2__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member, trigonal crystal form

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

2,3-dimethylmalate lyase

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

3fa3__assembly_2__model_1

3fa3__assembly_2__model_1 | I(q)

3fa3__assembly_2__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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)