1eex

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

Method: X-RAY DIFFRACTION

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

PROPANEDIOL DEHYDRATASE

Klebsiella oxytoca

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PROPANEDIOL DEHYDRATASE × 2 （Q59471） PROPANEDIOL DEHYDRATASE × 2 （Q59472） POTASSIUM ION × 4 CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 S-1,2-PROPANEDIOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q59470_KLEOX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–554； UniProt 1–554 Author chain L； PDBConstruct 1–554； UniProt 1–554

PROPANEDIOL DEHYDRATASE

Klebsiella oxytoca

UniProt Q59471

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PROPANEDIOL DEHYDRATASE × 2 （Q59470） PROPANEDIOL DEHYDRATASE × 2 （Q59472） POTASSIUM ION × 4 CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 S-1,2-PROPANEDIOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q59471_KLEOX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–224； UniProt 1–224 Author chain E； PDBConstruct 1–224； UniProt 1–224

PROPANEDIOL DEHYDRATASE

Klebsiella oxytoca

UniProt Q59472

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	PROPANEDIOL DEHYDRATASE × 2 （Q59470） PROPANEDIOL DEHYDRATASE × 2 （Q59471） POTASSIUM ION × 4 CO-(ADENIN-9-YL-PENTYL)-COBALAMIN × 2 S-1,2-PROPANEDIOL × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q59472_KLEOX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–173； UniProt 1–173 Author chain M； PDBConstruct 1–173； UniProt 1–173

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	1eex
Deposition date deposition_date	2000-02-04
Structure title title	CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA
Keywords keywords	COENZYME B12, PROPANEDIOL, POTASSIUM ION, TIM BARREL, 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.

1eex__assembly_1__model_1

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

Download this curve (.dat)

1eex__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1eex__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.23 Å
Rg (electron density)	36.93 Å
Total Rg	37.26 Å
Atom count	13530
Residues	1732
Excluded volume	240680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1eex__assembly_1__model_1`	hexameric （6）	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 (7)

Entity 1 Entity 1 polymer

Description description	PROPANEDIOL DEHYDRATASE
Molecular weight formula_weight	60408.1 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,L
Atom count atom_count	15494

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDNPVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQCSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPNEID

Source Source

Source organism organism	Klebsiella oxytoca
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PROPANEDIOL DEHYDRATASE
Molecular weight formula_weight	24141.7 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MEINEKLLRQIIEDVLSEMKGSDKPVSFNAPAASAAPQATPPAGDGFLTEVGEARQGTQQDEVIIAVGPAFGLAQTVNIVGIPHKSILREVIAGIEEEGIKARVIRCFKSSDVAFVAVEGNRLSGSGISIGIQSKGTTVIHQQGLPPLSNLELFPQAPLLTLETYRQIGKNAARYAKRESPQPVPTLNDQMARPKYQAKSAILHIKETKYVVTGKNPQELRVAL

Source Source

Source organism organism	Klebsiella oxytoca
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	PROPANEDIOL DEHYDRATASE
Molecular weight formula_weight	19198.7 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,M

MNTDAIESMVRDVLSRMNSLQGEAPAAAPAAGGASRSARVSDYPLANKHPEWVKTATNKTLDDFTLENVLSNKVTAQDMRITPETLRLQASIAKDAGRDRLAMNFERAAELTAVPDDRILEIYNALRPYRSTKEELLAIADDLESRYQAKICAAFVREAATLYVERKKLKGDD

Source Source

Source organism organism	Klebsiella oxytoca
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CO-(ADENIN-9-YL-PENTYL)-COBALAMIN
Molecular weight formula_weight	1537.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	S-1,2-PROPANEDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1872

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1eexa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.3 — Diol dehydratase, alpha subunit

Domain ID domain_id	d1eexb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
Family Family family	c.51.3.1 — Diol dehydratase, beta subunit

Domain ID domain_id	d1eexe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.3 — B12-dependent dehydatase associated subunit
Family Family family	c.51.3.1 — Diol dehydratase, beta subunit

Domain ID domain_id	d1eexg_
Class class	a — All alpha proteins
Fold Fold fold	a.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
Family Family family	a.23.2.1 — Diol dehydratase, gamma subunit

Domain ID domain_id	d1eexl_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.19 — Cobalamin (vitamin B12)-dependent enzymes
Family Family family	c.1.19.3 — Diol dehydratase, alpha subunit

Domain ID domain_id	d1eexm_
Class class	a — All alpha proteins
Fold Fold fold	a.23 — Open three-helical up-and-down bundle
Superfamily Superfamily superfamily	a.23.2 — Diol dehydratase, gamma subunit
Family Family family	a.23.2.1 — Diol dehydratase, gamma subunit

CATH v4.4 (6 domains)

Domain ID domain_id	1eexA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	350 — Diol/glycerol dehydratase, large subunit

Domain ID domain_id	1eexB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10150 — B12-dependent dehydatase associated subunit

Domain ID domain_id	1eexE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10150 — B12-dependent dehydatase associated subunit

Domain ID domain_id	1eexG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

Domain ID domain_id	1eexL00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	350 — Diol/glycerol dehydratase, large subunit

Domain ID domain_id	1eexM02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1510 — Hypothetical Protein Yqey; Chain: A; domain1
Homologous superfamily homologous superfamily	20 — Propanediol/glycerol dehydratase, small subunit

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Unit-cell length a length_a	73.380 Å
Unit-cell length b length_b	121.400 Å
Unit-cell length c length_c	207.600 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1640
R_work r_work	0.1610
R_free r_free	0.2260

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

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

PROPANEDIOL DEHYDRATASE

State in the Current Structure

Other States of the Same Protein in the Database

PROPANEDIOL DEHYDRATASE

State in the Current Structure

Other States of the Same Protein in the Database

PROPANEDIOL DEHYDRATASE

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

1eex__assembly_1__model_1

1eex__assembly_1__model_1 | I(q)

1eex__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)

CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

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

PROPANEDIOL DEHYDRATASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROPANEDIOL DEHYDRATASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROPANEDIOL DEHYDRATASE

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

1eex__assembly_1__model_1

1eex__assembly_1__model_1 | I(q)

1eex__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (2)