SAXSdb — 3gaj

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

Cobalamin adenosyltransferase PduO-like protein

Lactobacillus reuteri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	ADENOSINE-5'-TRIPHOSPHATE × 3 COBALAMIN × 3 POTASSIUM ION × 3 MAGNESIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q50EJ2_LACRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–187； UniProt 2–181

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	3gaj
Deposition date deposition_date	2009-02-17
Structure title title	Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP
Keywords keywords	TRANSFERASE; TRANSFERASE
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.

3gaj__assembly_1__model_1

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

Download this curve (.dat)

3gaj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gaj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.51 Å
Rg (electron density)	22.36 Å
Total Rg	23.29 Å
Atom count	4683
Residues	540
Excluded volume	82877 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gaj__assembly_1__model_1`	trimeric （3）	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	Cobalamin adenosyltransferase PduO-like protein
Molecular weight formula_weight	21533.4 kDa
EC 编号 ec_number	2.5.1.17
Mutation mutation	C-terminal truncation at residue 183
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1783

GASAPMVKIYTKNGDKGQTRIIGKQILYKNDPRVAAYGEVDELNSWVGYTKSLINSHTQVLSNELEEIQQLLFDCGHDLATPADDERHSFKFKQEQPTVWLEEKIDNYTQVVPAVKKFILPGGTQLASALHVARTITRRAERQIVQLMREEQINQDVLIFINRLSDYFFAAARYANYLEQQPDMLYR

Source Source

Source organism organism	Lactobacillus reuteri
NCBI taxonomy ID ncbi_taxonomy_id	1598
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	COBALAMIN
Molecular weight formula_weight	1330.4 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	167

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3gaja_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.2 — Cobalamin adenosyltransferase-like
Family Family family	a.25.2.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3gajA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

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Unit-cell length a length_a	67.679 Å
Unit-cell length b length_b	67.679 Å
Unit-cell length c length_c	111.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.380 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1650
R_work r_work	0.1640
R_free r_free	0.1820

Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP

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

Cobalamin adenosyltransferase PduO-like protein

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

3gaj__assembly_1__model_1

3gaj__assembly_1__model_1 | I(q)

3gaj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP

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

Cobalamin adenosyltransferase PduO-like protein

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

3gaj__assembly_1__model_1

3gaj__assembly_1__model_1 | I(q)

3gaj__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)