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- PDB-8e5s: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -

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Basic information

Entry
Database: PDB / ID: 8e5s
TitleX-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WT in an occluded 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 / 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)53,69532
Polymers44,5771
Non-polymers9,11831
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 area1210 Å2
ΔGint-11 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.658, 70.850, 98.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

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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, 78 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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.: 24 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / 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: 2.29 Å3/Da / Density % sol: 46.38 % / Description: 30 micron in size and isomorphous
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.7
Details: 28% PEG400, 0.1 M MES, pH 6.7, 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: 24-ID-C / Wavelength: 0.984 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.38→41.06 Å / Num. obs: 15678 / % possible obs: 93.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.73 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.099 / Rrim(I) all: 0.218 / Net I/σ(I): 7.4 / Num. measured all: 71063 / Scaling rejects: 210
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.38-2.471.238730416660.3770.6631.4161.895.9
8.91-41.060.06414053180.9960.0310.07221.787.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS1.20.1_4487data reduction
Aimless1.20.1_4487data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6C3I

6c3i


Resolution: 2.38→41.06 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 1565 10.02 %
Rwork0.2065 14059 -
obs0.2107 15624 91.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.28 Å2 / Biso mean: 48.0864 Å2 / Biso min: 22.03 Å2
Refinement stepCycle: final / Resolution: 2.38→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 434 47 3403
Biso mean--61.54 41.47 -
Num. residues----392
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.38-2.460.31261440.26391284142893
2.46-2.540.33761430.26131290143394
2.54-2.650.31831430.25151280142394
2.65-2.770.28631410.24771270141194
2.77-2.910.30641410.24041266140792
2.91-3.10.30591430.23941281142492
3.1-3.330.22951390.2351257139692
3.33-3.670.25441440.19091290143491
3.67-4.20.2251400.17391274141491
4.2-5.290.19391410.17431263140489
5.29-41.060.2261460.19041304145087
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)
14.90510.3801-1.0431.4217-1.44392.409-0.22750.2789-0.5043-0.4451-0.27590.27050.1970.12780.14060.55830.08050.01030.2323-0.02330.2054-14.9745-22.3230.3131
20.574-0.1850.07890.5535-0.89891.3989-0.0532-0.00610.0812-0.10690.0015-0.1078-0.04890.1120.0630.43380.0063-0.01710.21440.0220.1655-14.8842-13.416716.2637
32.32051.2475-0.22642.8143-0.54211.075-0.33340.182-0.2314-0.5410.1004-0.42770.20470.13460.22980.5070.04250.03780.28480.01590.3278-0.8678-26.244625.5401
41.23140.25730.16310.9495-0.91492.046-0.13230.0390.0429-0.1382-0.0680.06610.049-0.01830.0560.45310.02750.02340.2741-0.00160.1888-21.2037-20.691224.2557
50.5907-0.4040.05141.1243-0.83251.37580.0645-0.0252-0.2188-0.16810.1638-0.06440.28720.04030.09840.55760.03370.0360.24910.05110.2562-17.5188-27.34227.8147
60.8668-0.0615-0.16650.6739-0.70691.0977-0.07730.0038-0.08560.0038-0.0717-0.1573-0.00690.31640.15070.46260.00210.00520.210.00960.1993-7.3591-14.293922.3085
71.7349-0.147-0.09321.4146-0.2133.48140.0995-0.20460.1754-0.04380.19940.14150.0633-0.7545-0.01060.38680.0701-0.00170.31340.08110.1757-29.6192-11.503717.343
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 196 )A147 - 196
4X-RAY DIFFRACTION4chain 'A' and (resid 197 through 249 )A197 - 249
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 304 )A250 - 304
6X-RAY DIFFRACTION6chain 'A' and (resid 305 through 397 )A305 - 397
7X-RAY DIFFRACTION7chain 'A' and (resid 398 through 436 )A398 - 436

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