1mmf

Crystal structure of substrate free form of glycerol dehydratase

Method: X-RAY DIFFRACTION

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

glycerol dehydrase alpha subunit

Klebsiella pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	glycerol dehydrase beta subunit × 1 （O08505） glycerol dehydrase gamma subunit × 1 （Q59475） POTASSIUM ION × 1 COBALAMIN × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	glycerol dehydrase beta subunit × 1 （O08505） glycerol dehydrase gamma subunit × 1 （Q59475） POTASSIUM ION × 1 COBALAMIN × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	glycerol dehydrase beta subunit × 2 （O08505） glycerol dehydrase gamma subunit × 2 （Q59475） POTASSIUM ION × 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	Q59476_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–555； UniProt 1–555 Author chain L； PDBConstruct 1–555； UniProt 1–555

glycerol dehydrase beta subunit

Klebsiella pneumoniae

UniProt O08505

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	glycerol dehydrase alpha subunit × 1 （Q59476） glycerol dehydrase gamma subunit × 1 （Q59475） POTASSIUM ION × 1 COBALAMIN × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	glycerol dehydrase alpha subunit × 1 （Q59476） glycerol dehydrase gamma subunit × 1 （Q59475） POTASSIUM ION × 1 COBALAMIN × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	glycerol dehydrase alpha subunit × 2 （Q59476） glycerol dehydrase gamma subunit × 2 （Q59475） POTASSIUM ION × 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	O08505_KLEPN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–194； UniProt 2–194 Author chain E； PDBConstruct 1–194； UniProt 2–194

glycerol dehydrase gamma subunit

Klebsiella pneumoniae

UniProt Q59475

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	glycerol dehydrase alpha subunit × 1 （Q59476） glycerol dehydrase beta subunit × 1 （O08505） POTASSIUM ION × 1 COBALAMIN × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	glycerol dehydrase alpha subunit × 1 （Q59476） glycerol dehydrase beta subunit × 1 （O08505） POTASSIUM ION × 1 COBALAMIN × 1 water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	glycerol dehydrase alpha subunit × 2 （Q59476） glycerol dehydrase beta subunit × 2 （O08505） POTASSIUM ION × 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	Q59475_KLEPN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–141； UniProt 1–141 Author chain M； PDBConstruct 1–141； UniProt 1–141

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	1mmf
Deposition date deposition_date	2002-09-03
Structure title title	Crystal structure of substrate free form of glycerol dehydratase
Keywords keywords	Glycerol dehydratase, Diol dehydratase, Coenzyme B12, 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.

1mmf__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1mmf__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mmf__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	37.72 Å
Rg (electron density)	37.26 Å
Total Rg	37.53 Å
Atom count	13575
Residues	1735
Excluded volume	240920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mmf__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1mmf__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1mmf__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	glycerol dehydrase alpha subunit
Molecular weight formula_weight	60714.6 kDa
EC 编号 ec_number	4.2.1.30
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	13782

MKRSKRFAVLAQRPVNQDGLIGEWPEEGLIAMDSPFDPVSSVKVDNGLIVELDGKRRDQFDMIDRFIADYAINVERTEQAMRLEAVEIARMLVDIHVSREEIIAITTAITPAKAVEVMAQMNVVEMMMALQKMRARRTPSNQCHVTNLKDNPVQIAADAAEAGIRGFSEQETTVGIARYAPFNALALLVGSQCGRPGVLTQCSVEEATELELGMRGLTSYAETVSVYGTEAVFTDGDDTPWSKAFLASAYASRGLKMRYTSGTGSEALMGYSESKSMLYLESRCIFITKGAGVQGLQNGAVSCIGMTGAVPSGIRAVLAENLIASMLDLEVASANDQTFSHSDIRRTARTLMQMLPGTDFIFSGYSAVPNYDNMFAGSNFDAEDFDDYNILQRDLMVDGGLRPVTEAETIAIRQKAARAIQAVFRELGLPPIADEEVEAATYAHGSNEMPPRNVVEDLSAVEEMMKRNITGLDIVGALSRSGFEDIASNILNMLRQRVTGDYLQTSAILDRQFEVVSAVNDINDYQGPGTGYRISAERWAEIKNIPGVVQPDTIE

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	glycerol dehydrase beta subunit
Molecular weight formula_weight	21353.4 kDa
EC 编号 ec_number	4.2.1.30
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VQQTTQIQPSFTLKTREGGVASADERADEVVIGVGPAFDKHQHHTLIDMPHGAILKELIAGVEEEGLHARVVRILRTSDVSFMAWDAANLSGSGIGIGIQSKGTTVIHQRDLLPLSNLELFSQAPLLTLETYRQIGKNAARYARKESPSPVPVVNDQMVRPKFMAKAALFHIKETKHVVQDAEPVTLHIDLVRE

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	glycerol dehydrase gamma subunit
Molecular weight formula_weight	16128.4 kDa
EC 编号 ec_number	4.2.1.30
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSEKTMRVQDYPLATRCPEHILTPTGKPLTDITLEKVLSGEVGPQDVRISRQTLEYQAQIAEQMQRHAVARNFRRAAELIAIPDERILAIYNALRPFRSSQAELLAIADELEHTWHATVNAAFVRESAEVYQQRHKLRKGS

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

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	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	207

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1mmfa_
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	d1mmfb_
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	d1mmfe_
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	d1mmfg_
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	d1mmfl_
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	d1mmfm_
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	1mmfA00
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	1mmfB00
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	1mmfE00
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	1mmfG02
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	1mmfL00
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	1mmfM02
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	93.700 Å
Unit-cell length b length_b	110.070 Å
Unit-cell length c length_c	114.690 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.64 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2280
R_free r_free	0.2690

Crystal structure of substrate free form of glycerol dehydratase

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

glycerol dehydrase alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

glycerol dehydrase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

glycerol 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

1mmf__assembly_3__model_1

1mmf__assembly_3__model_1 | I(q)

1mmf__assembly_3__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of substrate free form of glycerol dehydratase

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

glycerol 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

glycerol 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

glycerol 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

1mmf__assembly_3__model_1

1mmf__assembly_3__model_1 | I(q)

1mmf__assembly_3__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)