7xrk

Diol dehydratase complexed with AdoMeCbl

Method: X-RAY DIFFRACTION

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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 × 2 (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 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

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 × 2 (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 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

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 × 2 (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol × 2 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

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	7xrk
Deposition date deposition_date	2022-05-10
Structure title title	Diol dehydratase complexed with AdoMeCbl
Keywords keywords	Adenosylcobalamin, Radical enzyme, 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.

7xrk__assembly_1__model_1

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

Download this curve (.dat)

7xrk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7xrk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.52 Å
Rg (electron density)	37.24 Å
Total Rg	37.57 Å
Atom count	13532
Residues	1732
Excluded volume	240490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7xrk__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 (8)

Entity 1 Entity 1 polymer

Description description	Diol dehydrase alpha subunit
Molecular weight formula_weight	60410.1 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,D
Atom count atom_count	13940

MRSKRFEALAKRPVNQDGFVKEWIEEGFIAMESPNDPKPSIKIVNGAVTELDGKPVSDFDLIDHFIARYGINLNRAEEVMAMDSVKLANMLCDPNVKRSEIVPLTTAMTPAKIVEVVSHMNVVEMMMAMQKMRARRTPSQQAHVTNVKDNPVQIAADAAEGAWRGFDEQETTVAVARYAPFNAIALLVGSQVGRPGVLTQCSLEEATELKLGMLGHTCYAETISVYGTEPVFTDGDDTPWSKGFLASSYASRGLKMRFTSGSGSEVQMGYAEGKSMLYLEARCIYITKAAGVQGLQNGSVSCIGVPSAVPSGIRAVLAENLICSSLDLECASSNDQTFTHSDMRRTARLLMQFLPGTDFISSGYSAVPNYDNMFAGSNEDAEDFDDYNVIQRDLKVDGGLRPVREEDVIAIRNKAARALQAVFAGMGLPPITDEEVEAATYAHGSKDMPERNIVEDIKFAQEIINKNRNGLEVVKALAQGGFTDVAQDMLNIQKAKLTGDYLHTSAIIVGDGQVLSAVNDVNDYAGPATGYRLQGERWEEIKNIPGALDPNEDD

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	2

Polymer Polymer

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

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	2

Polymer Polymer

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

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	2

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	2

Entity 6 Entity 6 non-polymer

Description description	(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-ethyl-oxolane-3,4-diol
Molecular weight formula_weight	265.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	408

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Unit-cell length a length_a	72.313 Å
Unit-cell length b length_b	111.564 Å
Unit-cell length c length_c	197.058 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	orthorhombic

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.070 Å
R factor r_factor	0.1667
R_work r_work	0.1651
R_free r_free	0.2251

Diol dehydratase complexed with AdoMeCbl

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

Diol dehydrase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Diol dehydrase gamma subunit

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

7xrk__assembly_1__model_1

7xrk__assembly_1__model_1 | I(q)

7xrk__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 (8)

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 water

7. Citations (1)

Diol dehydratase complexed with AdoMeCbl

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

7xrk__assembly_1__model_1

7xrk__assembly_1__model_1 | I(q)

7xrk__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 (8)

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 water

7. Citations (1)