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- PDB-8e6n: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -

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Basic information

Entry
Database: PDB / ID: 8e6n
TitleX-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter G223W mutant in an outward-open, manganese-bound state
ComponentsDivalent metal cation transporter MntH
KeywordsMETAL TRANSPORT / Membrane protein / divalent transition metal importer / LeuT fold / NRAMP family
Function / homology
Function and homology information


manganese ion transmembrane transporter activity / cadmium ion transmembrane transporter activity / symporter activity / cellular response to iron ion / metal ion binding / 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 / SPERMIDINE / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBozzi, A.T. / Ray, S. / Zimanyi, C.M. / Nicoludis, J.M. / Gaudet, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120996 United States
CitationJournal: Elife / Year: 2023
Title: High-resolution structures with bound Mn 2+ and Cd 2+ map the metal import pathway in an Nramp transporter.
Authors: Ray, S. / Berry, S.P. / Wilson, E.A. / Zhang, C.H. / Shekhar, M. / Singharoy, A. / Gaudet, R.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionMay 3, 2023ID: 6BU5
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Divalent metal cation transporter MntH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,72327
Polymers44,4811
Non-polymers7,24326
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, ITC shows micromolar affinity towards manganese
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint10 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.758, 80.389, 51.754
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-502-

MN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Divalent metal cation transporter MntH


Mass: 44480.680 Da / Num. of mol.: 1 / Mutation: G223W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: mntH, DR_1709 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RTP8

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Non-polymers , 5 types, 80 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 356.540 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.95 % / Description: 40 micron in size
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6
Details: 50 mM succinic acid, 10 mM spermidine, 5 mM manganese chloride, 100 mM MES, 28% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→39.19 Å / Num. obs: 13962 / % possible obs: 82.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 58.94 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.095 / Rrim(I) all: 0.21 / Net I/σ(I): 6.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 621 / CC1/2: 0.58 / % possible all: 36.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C3I

6c3i


Resolution: 2.4→39.19 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 701 5.02 %
Rwork0.2238 13259 -
obs0.2262 13960 82.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.45 Å2 / Biso mean: 74.9973 Å2 / Biso min: 37.12 Å2
Refinement stepCycle: final / Resolution: 2.4→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 244 54 3310
Biso mean--88.04 65.83 -
Num. residues----398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.590.3144860.2616152047
2.59-2.850.33851350.2809242976
2.85-3.260.27941490.2468294692
3.26-4.10.30271630.2295317798
4.1-39.190.23991680.2048318798
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)
13.99920.77010.98220.67690.91251.2054-0.0490.12480.0640.137-0.0036-0.04220.03080.19590.05850.34490.0254-0.05060.45160.05630.4147-23.5587-47.325215.6128
28.8909-5.4273-0.65456.4716-1.18337.20780.9628-0.9259-0.26021.1015-0.371-0.99810.54230.2186-0.32380.7993-0.1093-0.30830.62870.1090.7149-27.9113-56.654232.771
34.06980.59621.93492.3826-0.32252.73130.03910.06050.1654-0.0347-0.03990.04080.140.103-0.01120.32630.05340.00190.3662-0.03620.1659-26.5781-55.03079.255
46.21223.28551.69482.21461.0951.90310.0793-0.20150.034-0.1372-0.11550.16720.1207-0.25740.17040.40550.0566-0.07220.52580.03870.3421-33.6085-50.592524.2641
57.7778-3.3211.114.70760.07773.73320.3135-1.1983-0.1056-0.2844-0.14580.2774-0.56780.1584-0.13480.513-0.1288-0.08880.45380.02250.3631-21.2241-37.70059.4001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 146 )A39 - 146
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 171 )A147 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 286 )A172 - 286
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 369 )A287 - 369
5X-RAY DIFFRACTION5chain 'A' and (resid 370 through 436 )A370 - 436

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