3ez4

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei

Method: X-RAY DIFFRACTION

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

3-methyl-2-oxobutanoate hydroxymethyltransferase

Burkholderia pseudomallei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 5 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PANB_BURPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–269； UniProt 12–271 Author chain B； PDBConstruct 10–269； UniProt 12–271 Author chain C； PDBConstruct 10–269； UniProt 12–271 Author chain D； PDBConstruct 10–269； UniProt 12–271 Author chain E； PDBConstruct 10–269； UniProt 12–271 Author chain F； PDBConstruct 10–269； UniProt 12–271 Author chain G； PDBConstruct 10–269； UniProt 12–271 Author chain H； PDBConstruct 10–269； UniProt 12–271 Author chain I； PDBConstruct 10–269； UniProt 12–271 Author chain J； PDBConstruct 10–269； UniProt 12–271

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	3ez4
Deposition date deposition_date	2008-10-22
Structure title title	Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei
Keywords keywords	;Cytoplasm, Magnesium, Metal-binding, Methyltransferase, Pantothenate biosynthesis, Transferase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID ;; TRANSFERASE
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.

3ez4__assembly_1__model_1

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

Download this curve (.dat)

3ez4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ez4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.29 Å
Rg (electron density)	40.19 Å
Total Rg	40.63 Å
Atom count	17935
Residues	2433
Excluded volume	321240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ez4__assembly_1__model_1`	decameric （10）	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	3-methyl-2-oxobutanoate hydroxymethyltransferase
Molecular weight formula_weight	28542.8 kDa
EC 编号 ec_number	2.1.2.11
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	19382

MAHHHHHHMVTVPKLQAMREAGEKIAMLTSYDASFAALLDRANVDVQLIGDSLGNVLQGQATTLPVTLDDIAYHTACVARAQPRGLVVADLPFGTYGTPADAFASAVKLMRAGAQMVKLEGGEWLAETVRFLVERAVPVCAHVGLTPQSVHAFGGFKVQGKTEAGAAQLLRDARAVEEAGAQLIVLEAVPTLVAAEVTRELSIPTIGIGAGAECSGQVLVLHDMLGVFPGKRPRFVKDFMQGQPSIFAAVEAYVRAVKDGSFPGPEHSF

Source Source

Source organism organism	Burkholderia pseudomallei
Common name common_name	Pseudomonas pseudomallei
NCBI taxonomy ID ncbi_taxonomy_id	28450
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1447

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d3ez4a1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4a2
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	d3ez4b1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4b2
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	d3ez4c1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4c2
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	d3ez4d1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4d2
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	d3ez4e1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4e2
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	d3ez4f1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4f2
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	d3ez4g1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4g2
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	d3ez4h1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4h2
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	d3ez4i1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4i2
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	d3ez4j1
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.1.12.8 — Ketopantoate hydroxymethyltransferase PanB

Domain ID domain_id	d3ez4j2
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 (10 domains)

Domain ID domain_id	3ez4A00
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	3ez4B00
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	3ez4C00
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	3ez4D00
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	3ez4E00
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	3ez4F00
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	3ez4G00
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	3ez4H00
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	3ez4I00
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	3ez4J00
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	173.784 Å
Unit-cell length b length_b	187.556 Å
Unit-cell length c length_c	83.493 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	40

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	38.550 Å
R factor r_factor	0.1970
R_work r_work	0.1950
R_free r_free	0.2440

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei

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

3-methyl-2-oxobutanoate hydroxymethyltransferase

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

3ez4__assembly_1__model_1

3ez4__assembly_1__model_1 | I(q)

3ez4__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) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei

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

3-methyl-2-oxobutanoate hydroxymethyltransferase

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

3ez4__assembly_1__model_1

3ez4__assembly_1__model_1 | I(q)

3ez4__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) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)