SAXSdb — 2bb3

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

cobalamin biosynthesis precorrin-6Y methylase (cbiE)

Archaeoglobus fulgidus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O29536_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–219； UniProt 1–197 Author chain B； PDBConstruct 23–219； UniProt 1–197

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	2bb3
Deposition date deposition_date	2005-10-17
Structure title title	Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus
Keywords keywords	;beta, alpha-beta-alpha sandwich, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

2bb3__assembly_1__model_1

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

Download this curve (.dat)

2bb3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bb3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.64 Å
Rg (electron density)	21.24 Å
Total Rg	22.03 Å
Atom count	3110
Residues	380
Excluded volume	55431 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bb3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bb3__assembly_2__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	cobalamin biosynthesis precorrin-6Y methylase (cbiE)
Molecular weight formula_weight	25248.8 kDa
EC 编号 ec_number	2.1.1.-
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	3503

MGSSHHHHHHSSGRENLYFSGHMIWIVGSGTCRGQTTERAKEIIERAEVIYGSRRALELAGVVDDSRARILRSFKGDEIRRIMEEGREREVAVISTGDPMVAGLGRVLREIAEDVEIKIEPAISSVQVALARLKVDLSEVAVVDCHAKDFDAELTELLKYRHLLILADSHFPLERLGKRRVVLLENLCMEGERIREGNADSIELESDYTIIFVEREVMEGS

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	224325
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 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	180

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2bb3a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.90 — Tetrapyrrole methylase
Superfamily Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
Family Family family	c.90.1.1 — Tetrapyrrole methylase

Domain ID domain_id	d2bb3a2
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	d2bb3b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.90 — Tetrapyrrole methylase
Superfamily Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
Family Family family	c.90.1.1 — Tetrapyrrole methylase

Domain ID domain_id	d2bb3b3
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

CATH v4.4 (4 domains)

Domain ID domain_id	2bb3A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

Domain ID domain_id	2bb3A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

Domain ID domain_id	2bb3B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

Domain ID domain_id	2bb3B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

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Unit-cell length a length_a	88.191 Å
Unit-cell length b length_b	88.418 Å
Unit-cell length c length_c	115.932 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	2.270 Å
Low-resolution limit resolution_low	29.100 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2740

Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus

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

cobalamin biosynthesis precorrin-6Y methylase (cbiE)

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

2bb3__assembly_1__model_1

2bb3__assembly_1__model_1 | I(q)

2bb3__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus

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

cobalamin biosynthesis precorrin-6Y methylase (cbiE)

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

2bb3__assembly_1__model_1

2bb3__assembly_1__model_1 | I(q)

2bb3__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 (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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)