1o68

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase

Method: X-RAY DIFFRACTION

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

3-methyl-2-oxobutanoate hydroxymethyltransferase

Neisseria meningitidis serogroup B

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	SODIUM ION × 4 3-METHYL-2-OXOBUTANOIC ACID × 4 water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 10	SODIUM ION × 8 3-METHYL-2-OXOBUTANOIC ACID × 8 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PANB_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–265； UniProt 2–263 Author chain B； PDBConstruct 4–265； UniProt 2–263 Author chain C； PDBConstruct 4–265； UniProt 2–263 Author chain D； PDBConstruct 4–265； UniProt 2–263 Author chain E； PDBConstruct 4–265； UniProt 2–263

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	1o68
Deposition date deposition_date	2003-10-23
Structure title title	Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase
Keywords keywords	structural genomics, transferase; 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.

1o68__assembly_2__model_1

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

Download this curve (.dat)

1o68__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1o68__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	40.05 Å
Rg (electron density)	39.43 Å
Total Rg	39.72 Å
Atom count	18440
Residues	2388
Excluded volume	332710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1o68__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1o68__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	3-methyl-2-oxobutanoate hydroxymethyltransferase
Molecular weight formula_weight	29879.0 kDa
EC 编号 ec_number	2.1.2.11
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	9852

MSLITVNTLQKMKAAGEKIAMLTAYESSFAALMDDAGVEMLLVGDSLGMAVQGRKSTLPVSLRDMCYHTECVARGAKNAMIVSDLPFGAYQQSKEQAFAAAAELMAAGAHMVKLEGGVWMAETTEFLQMRGIPVCAHIGLTPQSVFAFGGYKVQGRGGKAQALLNDAKAHDDAGAAVVLMECVLAELAKKVTETVSCPTIGIGAGADCDGQVLVMHDMLGIFPGKTAKFVKNFMQGHDSVQAAVRAYVAEVKAKTFPAAEHIFADEGGSHHHHHH

Source Source

Source organism organism	Neisseria meningitidis serogroup B
NCBI taxonomy ID ncbi_taxonomy_id	491
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	4

Entity 3 Entity 3 non-polymer

Description description	3-METHYL-2-OXOBUTANOIC ACID
Molecular weight formula_weight	116.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	583

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1o68a1
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	d1o68a2
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	d1o68b1
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	d1o68b2
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	d1o68c1
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	d1o68c2
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	d1o68d1
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	d1o68d2
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	d1o68e1
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	d1o68e2
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 (5 domains)

Domain ID domain_id	1o68A00
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	1o68B00
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	1o68C00
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	1o68D00
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	1o68E00
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	164.419 Å
Unit-cell length b length_b	111.238 Å
Unit-cell length c length_c	98.807 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	122.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	69.000 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	0.2240

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase

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

1o68__assembly_2__model_1

1o68__assembly_2__model_1 | I(q)

1o68__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase

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

1o68__assembly_2__model_1

1o68__assembly_2__model_1 | I(q)

1o68__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)