SAXSdb — 3m8b

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–614	Mutation：V10R1A	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 7 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；2.5% PEG3350,20 mM Bis Tris, 150 mM Magnesium acetate, 10 mM C8E4, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.44 Å R-free 0.248

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3M8B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NQE OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI Deposited 2003-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Not recorded	MG MAGNESIUM ION × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG 3350, magnesium acetate, bis-tris, n-octyl tetraoxyethylene , pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.232
1NQF OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, METHIONINE SUBSTIUTION CONSTRUCT FOR SE-MET SAD PHASING Deposited 2003-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Mutation：W317M, K319M, T321M, W516M, I518M, Y520M Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHELYENE, tris-(2-carboxyethyl)phosphine hydrochloride , pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.288
1NQG OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM Deposited 2003-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Not recorded	CA CALCIUM ION × 4 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.31 Å R-free 0.259
1NQH OUTER MEMBRANE COBALAMIN TRANSPORTER (BTUB) FROM E. COLI, WITH BOUND CALCIUM AND CYANOCOBALAMIN (VITAMIN B12) SUBSTRATE Deposited 2003-01-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Not recorded	CA CALCIUM ION × 4 CNC CYANOCOBALAMIN × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；PEG 3350, MAGNESIUM ACETATE, BIS-TRIS, N-OCTYL TETRAOXYETHYLENE, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.10 Å R-free 0.265
1UJW Structure of the complex between BtuB and Colicin E3 Receptor binding domain Deposited 2003-08-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–614（594 aa）	Not recorded	GP1 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose × 2 LIM 3-OXO-PENTADECANOIC ACID × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 7 AAE ACETOACETIC ACID × 1 GOL GLYCEROL × 8	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.75 Å R-free 0.293
2GSK Structure of the BtuB:TonB Complex Deposited 2006-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–614（590 aa）	Not recorded	CA CALCIUM ION × 2 CNC CYANOCOBALAMIN × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 4 OCT N-OCTANE × 3 HEX HEXANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.1；288 K；30% (v/v) PEG 300, 0.1M sodium acetate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 5.10	Resolution 2.10 Å R-free 0.251
2GUF In meso crystal structure of the cobalamin transporter, BtuB Deposited 2006-04-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Not recorded	MPG [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate × 11 FMT FORMIC ACID × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.95 Å R-free 0.225
2YSU Structure of the complex between BtuB and Colicin E2 receptor binding domain Deposited 2007-04-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–614（594 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.50 Å R-free 0.315
3M8D Crystal structure of spin-labeled BtuB V10R1 with bound calcium and cyanocobalamin Deposited 2010-03-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Mutation：V10R1A	CNC CYANOCOBALAMIN × 1 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；2.5% PEG3350, 150 mM calcium chloride, 20 mM Bis tris, 10 mM C8E4, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.44 Å R-free 0.275
3RGM Crystal structure of spin-labeled BtuB T156R1 Deposited 2011-04-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Mutation：T156R1	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 6 MG MAGNESIUM ION × 9 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；3.0% PEG3350, 200 mM magnesium acetate, 10mM C8E4, 20 mM Bis Tris pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.60 Å R-free 0.254
3RGN Crystal structure of spin-labeled BtuB W371R1 Deposited 2011-04-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–614（594 aa）	Mutation：W371R1	C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 7 MG MAGNESIUM ION × 3 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；290 K；3.0% PEG3350, 200 mM magnesium acetate, 10 mM C8E4, 20 mM Bis Tris pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.30 Å R-free 0.250
7NSU ColicinE9 intact translocation complex Deposited 2021-03-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain F 21–614（594 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；3 uL of diluted translocon preparation were applied on freshly glow discharged grids coated with graphene oxide (as described in https://doi.org/10.1038/s41594-019-0355-2); after 30sec waiting grids were blotted for 8-10 using -10 force and plunge frozen in liquid ethane	Resolution 4.70 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

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	3m8b
Deposition date deposition_date	2010-03-17
Structure title title	Crystal structure of spin-labeled BtuB V10R1 in the apo state
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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.20 Å
Radius of gyration Rg (electron density) rg_electron	23.48 Å
Forward intensity I(0) i0	66286200.00
Molecular weight molecular_weight	63498.0 kDa
Excluded volume excluded_volume	79386 Å³
Envelope volume envelope_volume	98667 Å³
Hydration-shell volume shell_volume	33356 Å³
Envelope diameter envelope_diameter	78.5 Å
Shell Rg shell_rg	32.16 Å
Envelope Rg envelope_rg	23.65 Å
Shape Rg shape_rg	23.50 Å
Total Rg total_rg	24.37 Å
Total atoms total_atoms	4492
Residues n_residues	549
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	75.6 Å
Rg (real space) rg_real	23.99 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	6.6290e+07
I(0) uncertainty (real space) i0_real_error	8.5850e+05
Rg (reciprocal space) rg_reciprocal	24.04 Å
I(0) (reciprocal space) i0_reciprocal	66290000.0000
Solution quality estimate total_estimate	0.8899
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.087
Kurtosis Kurtosis kurtosis	-0.415
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15520000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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	4605

QDTSPDTLVCTANRFEQPRSTVLAPTTVVTRQDIDRWQSTSVNDVLRRLPGVDITQNGGSGQLSSIFIRGTNASHVLVLIDGVRLNLAGVSGSADLSQFPIALVQRVEYIRGPRSAVYGSDAIGGVVNIITTRDEPGTEISAGWGSNSYQNYDVSTQQQLGDKTRVTLLGDYAHTHGYDVVAYGNTGTQAQTDNDGFLSKTLYGALEHNFTDAWSGFVRGYGYDNRTNYDAYYSPGSPLLDTRKLYSQSWDAGLRYNGELIKSQLITSYSHSKDYNYDPHYGRYDSSATLDEMKQYTVQWANNVIVGHGSIGAGVDWQKQTTTPGTGYVEDGYDQRNTGIYLTGLQQVGDFTFEGAARSDDNSQFGRHGTWQTSAGWEFIEGYRFIASYGTSYKAPNLGQLYGFYGNPNLDPEKSKQWEGAFEGLTAGVNWRISGYRNDVSDLIDYDDHTLKYYNEGKARIKGVEATANFDTGPLTHTVSYDYVDARNAITDTPLLRRAKQQVKYQLDWQLYDFDWGITYQYLGTRYDKDYSSYPYQTVKMGGVSLWDLAVAYPVTSHLTVRGKIANLFDKDYETVYGYQTAGREYTLSGSYTF

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	113

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3m8ba_
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	3m8bA01
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	3m8bA02
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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8. Citations (1)

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Unit-cell length a length_a	81.290 Å
Unit-cell length b length_b	81.290 Å
Unit-cell length c length_c	226.562 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	44.130 Å
R factor r_factor	0.2210
R_work r_work	0.2190
R_free r_free	0.2480

fit	/app/data/saxs_computation/m8/3m8b/3m8b.fit
pddf	/app/data/pr_computation/m8/3m8b/3m8b.pr.out
profile	/app/data/saxs_computation/m8/3m8b/3m8b.dat

Crystal structure of spin-labeled BtuB V10R1 in the apo state

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction