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- PDB-10le: X-ray structure of the Bacteroides fragilis Nramp/MntH divalent t... -

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Basic information

Entry
Database: PDB / ID: 10le
TitleX-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, manganese-bound state
ComponentsDivalent metal cation transporter
KeywordsMETAL TRANSPORT / Membrane Protein / Divalent metal transporter / Manganese Homeostasis / Iron Homeostasis
Function / homology
Function and homology information


cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron ion transmembrane transport / symporter activity / plasma membrane
Similarity search - Function
NRAMP family / Natural resistance-associated macrophage protein-like
Similarity search - Domain/homology
: / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Divalent metal cation transporter
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRay, S. / Gaudet, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120996 United States
CitationJournal: To Be Published
Title: X-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, manganese-bound state
Authors: Ray, S. / Gaudet, R.
History
DepositionJan 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Divalent metal cation transporter
B: Divalent metal cation transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,43063
Polymers90,7852
Non-polymers20,64561
Water1,874104
1
A: Divalent metal cation transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,89332
Polymers45,3921
Non-polymers10,50131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Divalent metal cation transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,53731
Polymers45,3921
Non-polymers10,14430
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.853, 101.910, 118.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Divalent metal cation transporter / Metal ion (Mn2+/Fe2+) transporter (Nramp) family metal ion transporter / Nramp family divalent ...Metal ion (Mn2+/Fe2+) transporter (Nramp) family metal ion transporter / Nramp family divalent metal transporter


Mass: 45392.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: mntH, AC094_25680, BFGS077_004043, CQW34_02524, F2Z25_12705, F2Z29_10780, F2Z89_12735, F3B44_13840, FSA03_20375, FSA06_19765, FSA08_20470, NXW39_15865, NXX45_17380, O1420_13150
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K6BUR1
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase
Details: 0.2 M ammonium sulfate, 0.02 M sodium chloride, 0.02 M sodium acetate pH 4.0, 33% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.4→46.84 Å / Num. obs: 33378 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.78 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 33378 / CC1/2: 0.98 / Rpim(I) all: 0.248 / Rrim(I) all: 0.455 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.84 Å / SU ML: 0.3488 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.4527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2749 1999 5.99 %
Rwork0.2379 31379 -
obs0.2402 33378 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.64 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 806 104 6484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00176435
X-RAY DIFFRACTIONf_angle_d0.4238475
X-RAY DIFFRACTIONf_chiral_restr0.0367997
X-RAY DIFFRACTIONf_plane_restr0.0038975
X-RAY DIFFRACTIONf_dihedral_angle_d19.60822543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.40581420.36012225X-RAY DIFFRACTION99.41
2.46-2.530.37191380.3232179X-RAY DIFFRACTION99.61
2.53-2.60.34431420.30512211X-RAY DIFFRACTION99.7
2.6-2.680.36881400.29422207X-RAY DIFFRACTION99.91
2.68-2.780.32481410.28452213X-RAY DIFFRACTION99.92
2.78-2.890.3111420.26662225X-RAY DIFFRACTION100
2.89-3.020.31271410.26412220X-RAY DIFFRACTION99.87
3.02-3.180.28651420.25952230X-RAY DIFFRACTION100
3.18-3.380.26391410.23722223X-RAY DIFFRACTION99.96
3.38-3.640.24491450.21782274X-RAY DIFFRACTION99.88
3.64-4.010.24321420.19772213X-RAY DIFFRACTION99.7
4.01-4.590.22371460.18622283X-RAY DIFFRACTION99.84
4.59-5.780.23561450.21062289X-RAY DIFFRACTION99.88
5.78-46.840.24431520.21262387X-RAY DIFFRACTION98.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29652502838686-0.24495648195790.295290196823561.69941017168240.273141348050484.52102737177270.0308485292947540.0573514060078410.03256-0.174871809931990.034607853937023-0.10918-0.0924255395153160.211300672758460.0570920.184989596984960.04865386481328-0.193120362482140.300991984578050.0558770486370890.35724239855722-0.021-7.4627.153
20.7534724271599-0.178982648122710.519348233739782.20467444717630.197075071646670.96889991429240.085218355725890.121620452271140.0696543-0.20929972441111-0.050078343814415-0.09413-0.116687182158290.174388468908550.0060380.28928518215611-0.014911032546445-0.118319053452130.337044745115350.00461527910274220.409537474024981.6790.64133.575
30.38599863424269-1.0369307830315-0.140299375033452.77437297311710.452782966878810.26368630271320.1326802234190.12024424282774-0.066225-0.32951521438475-0.131765346318750.2050150.136282204232310.00272359497352820.00897530.32051201341798-0.014673988160161-0.204085706082450.37333595175447-0.00723899390127880.43757232345414-9.486-7.25124.572
40.179962529677810.018202374774579-0.888315694372470.41765480945892-0.518418407480234.7542192191092-0.0425783567676340.085487808665739-0.01422-0.089879995892007-0.10877849196040.072430.23673909501632-0.337809267183060.0647340.32867063891561-0.021470627711865-0.192662278902250.303788044224940.0528021244491990.32881838249165-34.05322.4927.22
50.37116174438001-0.057801381938254-0.295099450395190.63421958075146-0.238928385260271.1396548303096-0.00218558066131710.093124177669424-0-0.081125681326791-0.0346083506293270.077213-0.025889851976543-0.1583198309647-0.0240.26960235598011-0.0080404434659779-0.218695444503580.279294189285130.0241357618545330.32424058302284-35.8615.8133.122
60.360925397154690.15981351709595-0.120015790223920.77992033799165-0.748358167140440.8674932296731-0.078123946889384-0.048433350097310.000517-0.11556077211544-0.024076301643778-0.0150.0807694473068440.093201057126396-0.09971310.276421074183550.048481120546659-0.290409526241380.2252452401176-0.0338263198917310.26231739305368-28.63217.55527.975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:94 )A29 - 94
2X-RAY DIFFRACTION2( CHAIN A AND RESID 95:322 )A95 - 322
3X-RAY DIFFRACTION3( CHAIN A AND RESID 323:417 )A323 - 417
4X-RAY DIFFRACTION4( CHAIN B AND RESID 30:94 )B30 - 94
5X-RAY DIFFRACTION5( CHAIN B AND RESID 95:276 )B95 - 276
6X-RAY DIFFRACTION6( CHAIN B AND RESID 277:417 )B277 - 417

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