1wo8

Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8

Method: X-RAY DIFFRACTION

▼

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

methylglyoxal synthase

Thermus thermophilus HB8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 7 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 12	SULFATE ION × 14 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SHD6_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–126； UniProt 1–126 Author chain B； PDBConstruct 1–126； UniProt 1–126 Author chain C； PDBConstruct 1–126； UniProt 1–126 Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain E； PDBConstruct 1–126； UniProt 1–126 Author chain F； PDBConstruct 1–126； UniProt 1–126

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	1wo8
Deposition date deposition_date	2004-08-12
Structure title title	Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8
Keywords keywords	methylglyoxal synthase, Thermus thermophilus HB8, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

1wo8__assembly_1__model_1

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

Download this curve (.dat)

1wo8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wo8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.49 Å
Rg (electron density)	26.64 Å
Total Rg	27.52 Å
Atom count	5541
Residues	740
Excluded volume	100030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wo8__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wo8__assembly_2__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	methylglyoxal synthase
Molecular weight formula_weight	13397.7 kDa
EC 编号 ec_number	4.2.3.3
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	6357

MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKGTPQ

Source Source

Source organism organism	Thermus thermophilus HB8
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	816

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1wo8a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1wo8b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1wo8c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1wo8d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1wo8e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

Domain ID domain_id	d1wo8f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.24 — Methylglyoxal synthase-like
Superfamily Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
Family Family family	c.24.1.2 — Methylglyoxal synthase, MgsA

CATH v4.4 (6 domains)

Domain ID domain_id	1wo8A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1wo8B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1wo8C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1wo8D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1wo8E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

Domain ID domain_id	1wo8F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

▶

Unit-cell length a length_a	130.612 Å
Unit-cell length b length_b	130.612 Å
Unit-cell length c length_c	96.653 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	36

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	39.100 Å
R factor r_factor	0.1860
R_work r_work	0.1850
R_free r_free	0.2040

Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8

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

methylglyoxal synthase

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

1wo8__assembly_1__model_1

1wo8__assembly_1__model_1 | I(q)

1wo8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8

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

methylglyoxal synthase

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

1wo8__assembly_1__model_1

1wo8__assembly_1__model_1 | I(q)

1wo8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)