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- PDB-8e6i: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -

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Basic information

Entry
Database: PDB / ID: 8e6i
TitleX-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter M230A 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 / DI(HYDROXYETHYL)ETHER / Divalent metal cation transporter MntH
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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)53,00429
Polymers44,5171
Non-polymers8,48728
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, ITC shows M230A Micromolar level affinity towards Mn
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-25 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.673, 71.350, 98.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Divalent metal cation transporter MntH


Mass: 44516.648 Da / Num. of mol.: 1 / Mutation: M230A
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, 97 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.: 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.: 23 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.32 Å3/Da / Density % sol: 46.9 % / Description: 30 micron in size
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.5
Details: 32% PEG400 , 0.1 M MES, pH 6.5, 50 mM succinic acid, pH 6.0, 20 mM spermidine, pH 7.0, 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: 2.52→45.32 Å / Num. obs: 14581 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 54.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.269 / Rpim(I) all: 0.09 / Rrim(I) all: 0.284 / Net I/σ(I): 7.3 / Num. measured all: 144823 / Scaling rejects: 1
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
2.52-2.6210.43.1861677316130.3911.0353.3530.899.9
9.09-45.328.90.04132343650.9990.0150.04434.299.4

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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: 2.52→45.32 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 1454 10 %
Rwork0.2249 13086 -
obs0.2289 14540 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.32 Å2 / Biso mean: 66.6583 Å2 / Biso min: 33.7 Å2
Refinement stepCycle: final / Resolution: 2.52→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 448 69 3433
Biso mean--77.71 61.33 -
Num. residues----392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.52-2.610.34921430.313212821425
2.61-2.710.33891420.297712811423
2.71-2.840.37971430.29912791422
2.84-2.990.31531440.271613011445
2.99-3.170.28711420.247512791421
3.18-3.420.27041450.247113091454
3.42-3.760.26531450.217212941439
3.76-4.310.21541450.195413181463
4.31-5.430.23261490.196413351484
5.43-45.320.26951560.209114081564
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)
10.40330.24270.33261.621-2.02145.05040.08990.02540.0661-0.2810.03360.21150.33-0.1134-0.02440.33120.04140.00430.2811-0.02090.3518-19.2431-19.737920.0949
20.85570.0874-0.26121.9657-1.17491.7217-0.11180.04650.0824-0.2439-0.0358-0.20310.16190.07050.10320.3978-0.00760.00580.348-0.03110.3746-10.2328-19.617323.7673
30.7634-0.20750.42551.915-1.33362.4821-0.0085-0.0115-0.1268-0.14440.0350.00570.076-0.05950.00350.28060.02760.01090.2817-0.01690.335-15.2053-17.58423.1
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 112 )A45 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 249 )A113 - 249
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 436 )A250 - 436

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