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- PDB-8e6l: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -

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Basic information

Entry
Database: PDB / ID: 8e6l
TitleX-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter D296A mutant in an inward-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 transport / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron ion transmembrane transport / symporter activity / 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 / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsRay, S. / 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
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)52,23826
Polymers44,5331
Non-polymers7,70525
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, ITC shows micromolar affinity of binding towards manganese
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-24 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.514, 71.640, 98.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Divalent metal cation transporter MntH


Mass: 44532.758 Da / Num. of mol.: 1 / Mutation: D296A
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, 46 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.33 Å3/Da / Density % sol: 47.14 % / Description: 30 micron in size
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.8
Details: 28% PEG400, 0.1 M HEPES, pH 6.8, 0.1 M sodium chloride, 10 mM manganese chloride

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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: Sep 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.11→45.32 Å / Num. obs: 7042 / % possible obs: 91.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 63.48 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.342 / Rpim(I) all: 0.173 / Rrim(I) all: 0.386 / Net I/σ(I): 5.7 / Num. measured all: 27288 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.11-3.3341.817504812480.4150.8932.0351.692.2
8.81-45.323.80.0512223230.9970.0260.05719.986.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8E5S

8e5s


Resolution: 3.12→45.32 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2725 910 13.01 %
Rwork0.2194 6087 -
obs0.2264 6997 89.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.79 Å2 / Biso mean: 68.0807 Å2 / Biso min: 31.4 Å2
Refinement stepCycle: final / Resolution: 3.12→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 323 21 3197
Biso mean--65.22 58.65 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.12-3.280.34261290.288786399291
3.28-3.490.32521270.260185598291
3.49-3.760.31861310.2504874100591
3.76-4.140.30091300.228186899891
4.14-4.740.24551280.199985698489
4.74-5.960.23011320.2159885101790
5.97-45.320.23611330.1783886101985
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)
12.6687-0.50140.52512.6184-1.49970.87830.38660.0505-0.0978-0.087-0.3060.69590.0977-0.0260.20510.21450.07780.11690.2602-0.14250.6341-14.128-24.464729.407
20.3164-0.48910.44982.408-2.27472.18140.50.2317-0.2069-0.4967-0.16920.9090.39250.2698-0.15320.2214-0.0268-0.00970.3147-0.11150.7052-15.5788-14.271317.4525
35.32780.2934-0.32372.477-1.03881.76860.2030.4266-0.0015-0.1562-0.3856-0.2985-0.01130.56480.24530.2749-0.10020.14291.04970.19830.59236.6576-19.14923.0967
41.2312-1.37830.88243.4289-1.70842.21320.27440.1179-0.00690.24570.24310.85840.0403-0.1188-0.36440.41970.0270.10540.2152-0.15570.5717-16.6044-30.856933.4067
52.90120.40741.09823.1504-2.02352.12550.28320.2832-0.13140.27360.23080.676-0.10080.5717-0.43810.36340.0043-0.02460.2555-0.04010.6494-18.3899-16.009322.6265
61.3422-0.3532-0.19382.1979-2.20272.47840.28540.12140.0456-0.47780.14150.93560.1276-0.0834-0.49770.453-0.0188-0.0970.4824-0.11640.612-18.7047-27.426226.7698
70.3369-0.08270.06041.4603-1.83832.74920.3748-0.06280.0241-0.0719-0.25880.3292-0.31480.93850.02980.1933-0.01990.02420.4565-0.07480.4316-7.4249-15.501123.5061
80.8563-0.43860.37831.2165-1.26441.51870.1289-0.2852-0.44660.10240.6340.91040.0799-0.95080.43470.46490.1122-0.17280.54490.50830.9725-29.6995-11.80717.8955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 70 )A45 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 146 )A71 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 171 )A147 - 171
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 214 )A172 - 214
5X-RAY DIFFRACTION5chain 'A' and (resid 215 through 249 )A215 - 249
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 299 )A250 - 299
7X-RAY DIFFRACTION7chain 'A' and (resid 300 through 397 )A300 - 397
8X-RAY DIFFRACTION8chain 'A' and (resid 398 through 436 )A398 - 436

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