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

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Basic information

Entry
Database: PDB / ID: 10ky
TitleX-ray structure of the Bacteroides fragilis Nramp/MntH divalent transition metal transporter WT in an inward-open, 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: 2.48 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, 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)107,86152
Polymers90,7852
Non-polymers17,07650
Water75742
1
A: Divalent metal cation transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,16227
Polymers45,3921
Non-polymers8,76926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Divalent metal cation transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,69925
Polymers45,3921
Non-polymers8,30724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.119, 102.272, 119.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,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-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.32 Å3/Da / Density % sol: 47 %
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: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.48→45.14 Å / Num. obs: 30582 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 46.14 Å2 / CC1/2: 0.99 / Net I/σ(I): 4.4
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 30582 / CC1/2: 0.99 / Rpim(I) all: 0.205 / Rrim(I) all: 0.398 / % 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: 2.48→45.14 Å / SU ML: 0.3981 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.4853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2985 1993 6.52 %
Rwork0.259 28589 -
obs0.2615 30582 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.49 Å2
Refinement stepCycle: LAST / Resolution: 2.48→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 802 42 6509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00146541
X-RAY DIFFRACTIONf_angle_d0.38858637
X-RAY DIFFRACTIONf_chiral_restr0.03611010
X-RAY DIFFRACTIONf_plane_restr0.00371001
X-RAY DIFFRACTIONf_dihedral_angle_d20.17282607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.540.42091380.38832002X-RAY DIFFRACTION98.8
2.54-2.610.38061410.37622006X-RAY DIFFRACTION99.72
2.61-2.690.39271410.35092020X-RAY DIFFRACTION99.54
2.69-2.770.37511410.32812024X-RAY DIFFRACTION99.95
2.77-2.870.35471400.31921996X-RAY DIFFRACTION99.72
2.87-2.990.3571420.3072026X-RAY DIFFRACTION99.63
2.99-3.120.37761400.30252024X-RAY DIFFRACTION99.77
3.12-3.290.31421420.27352031X-RAY DIFFRACTION99.77
3.29-3.490.28461420.25412033X-RAY DIFFRACTION99.82
3.49-3.760.28981410.23742039X-RAY DIFFRACTION99.59
3.76-4.140.27391440.22952050X-RAY DIFFRACTION99.55
4.14-4.740.22021440.20892074X-RAY DIFFRACTION99.64
4.74-5.970.28941470.24212091X-RAY DIFFRACTION99.82
5.97-45.140.26461500.22022173X-RAY DIFFRACTION98.27
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)
10.343470590063640.31714249799059-0.672025594301482.74072564259360.700819337306721.6685219951885-0.021494786665897-0.0281802969887760.18497745380672-0.7540778994837-0.313624158097270.6236161053692-0.23555498550776-0.442000315709730.238874162250330.290959109435030.11946083326266-0.0781444380184790.4897024352932-0.24994581691080.654446780580350.48492116972747-15.408581584631-20.759599327791
20.653933714727110.56209003572873-0.700251819540572.0756064047999-0.584476513828221.0646406335222-0.143940941057810.083507783902316-0.26116571714747-0.364606337574240.042747925725425-0.262742596767050.076441385599815-0.196043424029970.0466322690582660.300226989958320.0048714220973291-0.0101381152894960.42558770568424-0.16976306169130.441291515742784.1830304625518-16.687881553928-29.32151202384
30.0522694002369710.00135978393316380.0266240719178580.0654767542272230.0723594849258050.0521132188755340.34733138323380.026652281051718-0.45179109175436-0.137331652796480.668616094085910.22986064221476-0.2540826344391-0.065797587407276-0.133568151747620.76212138096919-0.023596468077475-0.114024767673940.56897162574515-0.0273316479812410.9071115255633.3841311980105-13.960917244312-41.201849499974
40.827594199039460.65885528309173-0.55403798646652.1782000440877-0.191880584208110.55601681510778-0.13640562415716-0.056380503402164-0.059210368612374-0.369230786844060.11479839364308-0.0982594382919910.06822248509232-0.0975862868887570.0408110675868680.30247761992387-0.030566207173804-0.0131683407558010.43136717842113-0.140863787876350.387489149139576.249410221729-14.920570756021-30.443991171145
50.427988932086120.0538937668532480.617335318497341.5702352148970.605746746300521.50183007118350.0286537114092080.0324700496497210.268568945031070.0064967977165223-0.0472758769584650.093881815562496-0.0337095808044560.152273062658310.02582585427930.30243489328674-0.00562935016554540.0732431311942240.44828125096363-0.149597437704680.4841311884525537.977007232512-40.753776493842-32.421140124144
60.418782617437650.11545002413677-0.350610093429381.8177982864220.540553005718971.3763756637167-0.069579804356802-0.0118660484665960.096160516624560.0182877208485180.00939461297742920.099934463506967-0.0806975430755830.0444843287697270.00599766427046790.305758462466920.00606802793494840.0269065052115820.42206764048795-0.15836782077970.5385495918142437.912395147414-31.16812684038-25.686489022597
71.7592200714136-1.6839555820854-1.57327253483062.0072163300621.10416158780281.59155617726790.465326440644470.314363676890950.2282353806487-0.603813335149950.57935051875802-0.0725382879166610.292599017958880.058732059163229-0.234997543712970.57173446922430.0703578972322090.133618434474260.42529240812579-0.330669205992540.8164125485183538.695026821011-37.877133340765-41.684541843204
81.11789597005980.391263033857010.916298809431912.6886861028358-0.342366829439250.805555690579260.030990431435295-0.0036764553592598-0.06056962263367-0.267335715884480.12701098076353-0.055244308776888-0.151116321599840.097525046096804-0.0328190824218780.279780484105530.0154158492043680.0536686272686240.48564941912736-0.0654618242697240.6015568608438442.398546880901-33.112488725396-23.7432598002
90.34289379607775-0.871426054976470.658849951038972.49603336345640.524118490454620.76659881918565-0.000809532055371190.1729197154610.0068420451357268-0.39448365439204-0.229207800237130.13241633127647-0.13883544354772-0.010678734774786-0.0356352291274380.33158109255322-0.023424096310.0266074557714050.45670671296851-0.0832677227368930.6573181110952528.976290975962-39.109631891188-36.091909439942
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 29 through 54 )AA29 - 541 - 26
22chain 'A' and (resid 55 through 209 )AA55 - 20927 - 181
33chain 'A' and (resid 210 through 236 )AA210 - 236182 - 193
44chain 'A' and (resid 237 through 417 )AA237 - 417194 - 374
55chain 'B' and (resid 29 through 94 )BAB29 - 941 - 66
66chain 'B' and (resid 95 through 209 )BAB95 - 20967 - 181
77chain 'B' and (resid 210 through 236 )BAB210 - 236182 - 194
88chain 'B' and (resid 237 through 323 )BAB237 - 323195 - 281
99chain 'B' and (resid 324 through 417 )BAB324 - 417282 - 375

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