5yrv

Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal

Method: X-RAY DIFFRACTION

▼

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

Diol dehydrase alpha subunit

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	Diol dehydrase beta subunit × 2 （Q59471） Diol dehydrase gamma subunit × 2 （Q59472） CALCIUM ION × 2 POTASSIUM ION × 4 S-1,2-PROPANEDIOL × 2 5'-DEOXYADENOSINE × 2 CHLORIDE ION × 6 COBALAMIN × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Diol dehydrase beta subunit × 2 （Q59471） Diol dehydrase gamma subunit × 2 （Q59472） CALCIUM ION × 2 POTASSIUM ION × 4 S-1,2-PROPANEDIOL × 1 5'-DEOXYADENOSINE × 2 CHLORIDE ION × 6 COBALAMIN × 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 D； PDBConstruct 1–554； UniProt 1–554 Author chain G； PDBConstruct 1–554； UniProt 1–554 Author chain J； PDBConstruct 1–554； UniProt 1–554

Diol dehydrase beta subunit

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	Diol dehydrase alpha subunit × 2 （Q59470） Diol dehydrase gamma subunit × 2 （Q59472） CALCIUM ION × 2 POTASSIUM ION × 4 S-1,2-PROPANEDIOL × 2 5'-DEOXYADENOSINE × 2 CHLORIDE ION × 6 COBALAMIN × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Diol dehydrase alpha subunit × 2 （Q59470） Diol dehydrase gamma subunit × 2 （Q59472） CALCIUM ION × 2 POTASSIUM ION × 4 S-1,2-PROPANEDIOL × 1 5'-DEOXYADENOSINE × 2 CHLORIDE ION × 6 COBALAMIN × 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 22–200； UniProt 46–224 Author chain E； PDBConstruct 22–200； UniProt 46–224 Author chain H； PDBConstruct 22–200； UniProt 46–224 Author chain K； PDBConstruct 22–200； UniProt 46–224

Diol dehydrase gamma subunit

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	Diol dehydrase alpha subunit × 2 （Q59470） Diol dehydrase beta subunit × 2 （Q59471） CALCIUM ION × 2 POTASSIUM ION × 4 S-1,2-PROPANEDIOL × 2 5'-DEOXYADENOSINE × 2 CHLORIDE ION × 6 COBALAMIN × 2 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Diol dehydrase alpha subunit × 2 （Q59470） Diol dehydrase beta subunit × 2 （Q59471） CALCIUM ION × 2 POTASSIUM ION × 4 S-1,2-PROPANEDIOL × 1 5'-DEOXYADENOSINE × 2 CHLORIDE ION × 6 COBALAMIN × 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 C； PDBConstruct 2–137； UniProt 38–173 Author chain F； PDBConstruct 2–137； UniProt 38–173 Author chain I； PDBConstruct 2–137； UniProt 38–173 Author chain L； PDBConstruct 2–137； UniProt 38–173

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5yrv
Deposition date deposition_date	2017-11-10
Structure title title	Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal
Keywords keywords	Adenosylcobalamin, Radical enzyme, 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.

5yrv__assembly_1__model_1

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

Download this curve (.dat)

5yrv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5yrv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.11 Å
Rg (electron density)	36.86 Å
Total Rg	37.18 Å
Atom count	13558
Residues	1734
Excluded volume	241230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5yrv__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5yrv__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Diol dehydrase alpha subunit
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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J
Atom count atom_count	30656

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDNPVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQCSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPNEID

Source Source

Source organism organism	Klebsiella oxytoca
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Diol dehydrase beta subunit
Molecular weight formula_weight	21721.9 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MSSHHHHHHSAALEVLFQGPGGFLTEVGEARQGTQQDEVIIAVGPAFGLAQTVNIVGIPHKSILREVIAGIEEEGIKARVIRCFKSSDVAFVAVEGNRLSGSGISIGIQSKGTTVIHQQGLPPLSNLELFPQAPLLTLETYRQIGKNAARYAKRESPQPVPTLNDQMARPKYQAKSAILHIKETKYVVTGKNPQELRVAL

Source Source

Source organism organism	Klebsiella oxytoca
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Diol dehydrase gamma subunit
Molecular weight formula_weight	15611.7 kDa
EC 编号 ec_number	4.2.1.28
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L

MARVSDYPLANKHPEWVKTATNKTLDDFTLENVLSNKVTAQDMRITPETLRLQASIAKDAGRDRLAMNFERAAELTAVPDDRILEIYNALRPYRSTKEELLAIADDLESRYQAKICAAFVREAATLYVERKKLKGDD

Source Source

Source organism organism	Klebsiella oxytoca
NCBI taxonomy ID ncbi_taxonomy_id	571
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	8

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	3

Entity 7 Entity 7 non-polymer

Description description	5'-DEOXYADENOSINE
Molecular weight formula_weight	251.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 9 Entity 9 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3299

▼

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d5yrva_
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	d5yrvb1
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	d5yrvb2
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	d5yrvc_
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	d5yrvd_
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	d5yrve_
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	d5yrvf_
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	d5yrvg_
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	d5yrvh_
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	d5yrvi_
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	d5yrvj_
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	d5yrvk1
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	d5yrvk2
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	d5yrvl_
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 (12 domains)

Domain ID domain_id	5yrvA00
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	5yrvB00
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	5yrvC02
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	5yrvD00
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	5yrvE00
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	5yrvF02
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	5yrvG00
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	5yrvH00
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	5yrvI02
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	5yrvJ00
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	5yrvK00
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	5yrvL02
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

▶

Unit-cell length a length_a	72.777 Å
Unit-cell length b length_b	95.666 Å
Unit-cell length c length_c	114.514 Å
Unit-cell angle α angle_alpha	80.61 °
Unit-cell angle β angle_beta	87.77 °
Unit-cell angle γ angle_gamma	81.25 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	44.000 Å
R factor r_factor	0.1555
R_work r_work	0.1552
R_free r_free	0.1813

Diol dehydratase, AdoCbl/1,2-propanediol, anaerobically-prepared crystal

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

Diol dehydrase alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Diol dehydrase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Diol dehydrase gamma subunit

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

5yrv__assembly_1__model_1

5yrv__assembly_1__model_1 | I(q)

5yrv__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 (10)

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

CATH v4.4 (12 domains)

7. Citations (1)