SAXSdb — 3m8d

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

Vitamin B12 transporter btuB

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CYANOCOBALAMIN × 1 (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 CALCIUM ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BTUB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–594； UniProt 21–614

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	3m8d
Deposition date deposition_date	2010-03-17
Structure title title	Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin
Keywords keywords	;beta barrel, R1, spin label, Cell membrane, Cell outer membrane, Ion transport, Membrane, Metal-binding, Phage recognition, Porin, Receptor, TonB box, Transmembrane, Transport, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
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.

3m8d__assembly_1__model_1

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

Download this curve (.dat)

3m8d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3m8d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.66 Å
Rg (electron density)	23.87 Å
Total Rg	24.80 Å
Atom count	4785
Residues	582
Excluded volume	84469 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3m8d__assembly_1__model_1`	monomeric （1）	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	Vitamin B12 transporter btuB
Molecular weight formula_weight	66390.2 kDa
Mutation mutation	V10R1A
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	4862

QDTSPDTLVCTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CYANOCOBALAMIN
Molecular weight formula_weight	1356.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
Molecular weight formula_weight	264.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3m8da_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.3 — Porins
Family Family family	f.4.3.3 — Ligand-gated protein channel

CATH v4.4 (2 domains)

Domain ID domain_id	3m8dA01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	130 — Ferric Hydroxamate Uptake Protein; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — TonB-dependent receptor, plug domain

Domain ID domain_id	3m8dA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	170 — Maltoporin; Chain A
Homologous superfamily homologous superfamily	20 — TonB-dependent receptor, beta-barrel domain

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Unit-cell length a length_a	82.051 Å
Unit-cell length b length_b	82.051 Å
Unit-cell length c length_c	224.457 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.440 Å
Low-resolution limit resolution_low	44.040 Å
R factor r_factor	0.2290
R_work r_work	0.2260
R_free r_free	0.2750

Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin

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

Vitamin B12 transporter btuB

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

3m8d__assembly_1__model_1

3m8d__assembly_1__model_1 | I(q)

3m8d__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin

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

Vitamin B12 transporter btuB

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

3m8d__assembly_1__model_1

3m8d__assembly_1__model_1 | I(q)

3m8d__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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)