SAXSdb — 4mtj

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

B12-independent glycerol dehydratase

Clostridium butyricum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	S-1,2-PROPANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8GEZ8_CLOBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–787； UniProt 1–787 Author chain B； PDBConstruct 1–787； UniProt 1–787

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	4mtj
Deposition date deposition_date	2013-09-19
Structure title title	Structure of the b12-independent glycerol dehydratase with 1,2-propanediol bound
Keywords keywords	PFL-like glycyl radical enzyme, glycerol/diol dehydratase, HYDROLASE; HYDROLASE
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.

4mtj__assembly_1__model_1

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

Download this curve (.dat)

4mtj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4mtj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.32 Å
Rg (electron density)	39.22 Å
Total Rg	39.63 Å
Atom count	12390
Residues	1572
Excluded volume	220220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4mtj__assembly_1__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	B12-independent glycerol dehydratase
Molecular weight formula_weight	88154.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	13286

MISKGFSTQTERINILKAQILNAKPCVESERAILITESFKQTEGQPAILRRALALKHILENIPITIRDQELIVGSLTKEPRSSQVFPEFSNKWLQDELDRLNKRTGDAFQISEESKEKLKDVFEYWNGKTTSELATSYMTEETREAVNCDVFTVGNYYYNGVGHVSVDYGKVLRVGFNGIINEAKEQLEKNRSIDPDFIKKEKFLNSVIISCEAAITYVNRYAKKAKEIADNTSDAKRKAELNEIAKICSKVSGEGAKSFYEACQLFWFIHAIINIESNGHSISPARFDQYMYPYYENDKNITDKFAQELIDCIWIKLNDINKVRDEISTKHFGGYPMYQNLIVGGQNSEGKDATNKVSYMALEAAVHVKLPQPSLSVRIWNKTPDEFLLRAAELTREGLGLPAYYNDEVIIPALVSRGLTLEDARDYGIIGCVEPQKPGKTEGWHDSAFFNLARIVELTINSGFDKNKQIGPKTQNFEEMKSFDEFMKAYKAQMEYFVKHMCCADNCIDIAHAERAPLPFLSSMVDNCIGKGKSLQDGGAEYNFSGPQGVGVANIGDSLVAVKKIVFDENKITPSELKKTLNNDFKNSEEIQALLKNAPKFGNDIDEVDNLAREGALVYCREVNKYTNPRGGNFQPGLYPSSINVYFGSLTGATPDGRKSGQPLADGVSPSRGCDVSGPTAACNSVSKLDHFIASNGTLFNQKFHPSALKGDNGLMNLSSLIRSYFDQKGFHVQFNVIDKKILLAAQKNPEKYQDLIVRVAGYSAQFISLDKSIQNDIIARTEHVM

Source Source

Source organism organism	Clostridium butyricum
NCBI taxonomy ID ncbi_taxonomy_id	1492

Entity 2 Entity 2 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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	896

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4mtja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.1 — PFL-like

Domain ID domain_id	d4mtjb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.1 — PFL-like

CATH v4.4 (2 domains)

Domain ID domain_id	4mtjA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4mtjB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	102.696 Å
Unit-cell length b length_b	212.399 Å
Unit-cell length c length_c	198.740 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	46.228 Å
R factor r_factor	0.1724
R_work r_work	0.1701
R_free r_free	0.2149

Structure of the b12-independent glycerol dehydratase with 1,2-propanediol bound

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

B12-independent glycerol 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

4mtj__assembly_1__model_1

4mtj__assembly_1__model_1 | I(q)

4mtj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the b12-independent glycerol dehydratase with 1,2-propanediol bound

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

B12-independent glycerol 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

4mtj__assembly_1__model_1

4mtj__assembly_1__model_1 | I(q)

4mtj__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)