SAXSdb — 10le

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

Divalent metal cation transporter

Bacteroides fragilis

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 14–417	Not recorded	MN MANGANESE (II) ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 29 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；298 K；0.2 M ammonium sulfate, 0.02 M sodium chloride, 0.02 M sodium acetate pH 4.0, 33% PEG 200	Resolution 2.40 Å R-free 0.275
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 14–417	Not recorded	MN MANGANESE (II) ION × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 28 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；298 K；0.2 M ammonium sulfate, 0.02 M sodium chloride, 0.02 M sodium acetate pH 4.0, 33% PEG 200	Resolution 2.40 Å R-free 0.275

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 10LE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10KY X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, state Deposited 2026-01-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–417（404 aa）	Not recorded	OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 24 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；298 K；0.2 M ammonium sulfate, 0.02 M sodium chloride, 0.02 M sodium acetate pH 4.0, 33% PEG 200	Resolution 2.48 Å R-free 0.298
10KY X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, state Deposited 2026-01-26	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–417（404 aa）	Not recorded	OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 23 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；298 K；0.2 M ammonium sulfate, 0.02 M sodium chloride, 0.02 M sodium acetate pH 4.0, 33% PEG 200	Resolution 2.48 Å R-free 0.298

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0K6BUR1_BACFG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–416； UniProt 14–417 Author chain B； PDBConstruct 13–416； UniProt 14–417

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	10le
Deposition date deposition_date	2026-01-26
最后修订 last_revision	2026-03-04
Structure title title	X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, manganese-bound state
Keywords keywords	Membrane Protein, Divalent metal transporter, Manganese Homeostasis, Iron Homeostasis, METAL TRANSPORT; METAL TRANSPORT
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	28.38 Å
Radius of gyration Rg (electron density) rg_electron	28.47 Å
Forward intensity I(0) i0	76818000.00
Molecular weight molecular_weight	90501.0 kDa
Excluded volume excluded_volume	122700 Å³
Envelope volume envelope_volume	140140 Å³
Hydration-shell volume shell_volume	39745 Å³
Envelope diameter envelope_diameter	99.6 Å
Shell Rg shell_rg	36.83 Å
Envelope Rg envelope_rg	28.96 Å
Shape Rg shape_rg	28.47 Å
Total Rg total_rg	29.48 Å
Total atoms total_atoms	6379
Residues n_residues	740
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	92.2 Å
Rg (real space) rg_real	28.31 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	7.6820e+07
I(0) uncertainty (real space) i0_real_error	1.1640e+06
Rg (reciprocal space) rg_reciprocal	28.33 Å
I(0) (reciprocal space) i0_reciprocal	76820000.0000
Solution quality estimate total_estimate	0.8986
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	90.6 Å
Skewness Skewness skewness	0.263
Kurtosis Kurtosis kurtosis	-0.452
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22730000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.968

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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	Divalent metal cation transporter
Molecular weight formula_weight	45392.4 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	6483

MHHHHHHHHAHMKRYLGGLDVFRYIGPGLLVTVGFIDPGNWASNFAAGSEFGYSLLWVVTLSTIMLIILQHNVAHLGIVTGLCLSEAATQYTPKWVSRPILGTAVLASISTSLAEILGGAIALEMLLDIPIVWGAVLTTVFVSIMLFTNSYKKIERSIIAFVSVIGLSFIYELFLVDIDWPMAVEGWVTPAIPKGSMLIIMSVLGAVVMPHNLFLHSEVIQSHEYNKQDTASIKKVLKYELFDTLFSMIIGWAINSAMILLAAATFFKSGIQVEELQQAKSLLEPLLGSNAAIVFALALLMAGISSTITSGMAAGSIFAGIFGESYHIKDSHSQVGVILSLGIALLLIFFIGDPFKGLIISQMVLSIQLPFTVFLQVGLTSSRKVMGDYVNSKWSTFVLYTIAVIVTVLNIMLLFS

来源 Source

来源生物 organism	Bacteroides fragilis
NCBI Class编号 ncbi_taxonomy_id	817
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	57

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

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8. Citations (1)

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Unit-cell length a length_a	68.853 Å
Unit-cell length b length_b	101.910 Å
Unit-cell length c length_c	118.895 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	8

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	46.840 Å
R factor r_factor	0.2402
R_work r_work	0.2379
R_free r_free	0.2749

fit	/app/data/saxs_computation/0l/10le/10le.fit
pddf	/app/data/pr_computation/0l/10le/10le.pr.out
profile	/app/data/saxs_computation/0l/10le/10le.dat

X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, manganese-bound state

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

Divalent metal cation transporter

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