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- PDB-8e60: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -

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Basic information

Entry
Database: PDB / ID: 8.0E+60
TitleX-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an occluded, 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 / DI(HYDROXYETHYL)ETHER / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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)53,33331
Polymers44,5771
Non-polymers8,75630
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, ITC with Mn shows micromolar level binding affinity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-10 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.076, 71.101, 98.747
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: 44576.766 Da / Num. of mol.: 1
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 , 6 types, 77 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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.: 23 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 47 / 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: 47.17 % / Description: 35 micron in size
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6
Details: 24% PEG400, 0.1 M MES, pH 5.9, 50 mM succinic acid, pH 6.0, 5 mM spermidine, pH 7.0

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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 EIGER2 X 16M / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.38→41.28 Å / Num. obs: 16467 / % possible obs: 96 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.064 / Rrim(I) all: 0.127 / Net I/σ(I): 8 / Num. measured all: 56770
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
2.38-2.473.51.292600817310.3670.7591.5110.998
8.91-41.283.30.02311333400.9990.0150.02836.390.9

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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 8E5V

8e5v


Resolution: 2.38→41.28 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 1642 10 %
Rwork0.2077 14781 -
obs0.2128 16423 95.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.57 Å2 / Biso mean: 64.9912 Å2 / Biso min: 27.21 Å2
Refinement stepCycle: final / Resolution: 2.38→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 405 47 3379
Biso mean--78.5 58.24 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.38-2.450.36871380.31261242138097
2.45-2.530.29911370.28791228136597
2.53-2.620.35821360.26771223135997
2.62-2.720.31061320.24971201133394
2.72-2.850.30331380.25231241137997
2.85-30.34531370.22891237137496
3-3.190.2741370.22471225136296
3.19-3.430.25571380.20831241137996
3.43-3.780.22071360.181227136395
3.78-4.320.20831350.18441216135193
4.32-5.440.25021380.17911246138493
5.45-41.280.2531400.20331254139489
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)
12.3464-0.0604-0.39812.618-2.51673.0375-0.18480.5096-0.13060.2033-0.1479-0.38650.766-0.23560.27070.4980.02310.02650.4123-0.02280.4721-15.5368-22.434830.5465
20.06580.05580.23230.9082-1.17143.2898-0.02490.00910.0246-0.1782-0.1292-0.22370.08950.30690.20780.35740.01940.00370.28810.04450.4106-15.1039-13.49716.2907
31.640.953-0.45032.9031-1.09552.1655-0.17410.0698-0.1547-0.1923-0.062-0.6280.02040.29970.28860.34170.00040.010.32660.050.3832-10.0465-24.219429.9882
43.47350.54421.98463.9159-0.2864.3993-0.13961.1426-0.5962-0.4072-0.1319-0.74351.44680.6938-0.04980.6831-0.05560.09990.5955-0.03740.546-16.4282-21.34997.3605
50.9157-0.75271.38572.1154-1.2378.5587-0.17990.0803-0.1209-0.60460.05850.14130.79180.2588-0.10230.5213-0.1070.00650.34720.04040.4554-21.4263-29.404819.5137
61.3538-0.53450.7972.8324-2.76593.48330.0519-0.0682-0.0465-0.446-0.5029-0.43140.45480.6680.44490.30280.0284-0.03160.43150.05080.4345-6.7659-22.612431.0228
70.74490.2889-0.26791.593-1.27332.74620.0305-0.0344-0.28660.0107-0.2074-0.4712-0.33850.74980.38040.3873-0.0737-0.03910.38640.03150.4624-8.99-9.410321.2479
82.4313-1.05660.26643.0519-0.7516.0678-0.1064-0.36840.0147-0.26010.23610.0743-0.1026-0.9716-0.06730.17660.0858-0.04240.34880.06770.3688-29.8237-11.51517.4049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 74 )A45 - 74
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 146 )A75 - 146
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 228 )A147 - 228
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 249 )A229 - 249
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 286 )A250 - 286
6X-RAY DIFFRACTION6chain 'A' and (resid 287 through 343 )A287 - 343
7X-RAY DIFFRACTION7chain 'A' and (resid 344 through 397 )A344 - 397
8X-RAY DIFFRACTION8chain 'A' and (resid 398 through 436 )A398 - 436

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