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- PDB-8e5v: X-ray structure of the Deinococcus radiodurans Nramp/MntH divalen... -

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Basic information

Entry
Database: PDB / ID: 8e5v
TitleX-ray structure of the Deinococcus radiodurans Nramp/MntH divalent transition metal transporter WTsoak 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: 2.36 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)54,47432
Polymers44,5771
Non-polymers9,89731
Water1,09961
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 area750 Å2
ΔGint-12 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.954, 71.037, 98.773
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 , 5 types, 92 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.: 27 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 47.02 % / Description: 40 micron in size
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 6.3
Details: 28% PEG400, 0.1 M MES, pH 6.3, 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 EIGER 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: 2.36→41.23 Å / Num. obs: 17464 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.97 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.069 / Rrim(I) all: 0.128 / Net I/σ(I): 5.8 / Num. measured all: 57927
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
2.36-2.453.41.328620518130.3890.8461.5810.799.5
8.83-41.233.10.02411733780.9980.0160.02925.396.9

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Processing

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

8e5s


Resolution: 2.36→41.23 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1743 10 %
Rwork0.2169 15689 -
obs0.2198 17432 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.48 Å2 / Biso mean: 65.1889 Å2 / Biso min: 31.76 Å2
Refinement stepCycle: final / Resolution: 2.36→41.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 443 61 3427
Biso mean--77.99 56.34 -
Num. residues----392
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 (%)
2.36-2.430.34731430.34571281142499
2.43-2.510.36331420.30331282142499
2.51-2.60.32171430.31285142899
2.6-2.70.32091450.2851298144399
2.7-2.820.32491450.263913121457100
2.82-2.970.28421440.23312971441100
2.97-3.160.30441450.224413051450100
3.16-3.40.24511470.21861316146399
3.4-3.750.22251440.2081297144198
3.75-4.290.20881440.18031302144698
4.29-5.40.20391500.18681345149599
5.4-41.230.22541510.2041369152096
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)
12.35970.4659-0.29182.0119-2.1572.7112-0.21120.7148-0.1424-0.0768-0.3373-0.34990.7586-0.33460.20640.47930.07340.00560.47140.02140.46-15.559-22.434830.5683
21.0094-0.00790.21091.9632-1.41033.35170.00940.05190.0797-0.1909-0.1135-0.01180.04640.25660.15820.29940.03420.02590.29230.00510.4162-14.9673-13.476816.4417
33.0984-0.4275-1.17937.15583.16373.7111-0.0089-0.4040.2563-1.51210.1083-0.62830.00671.0610.54470.63430.033-0.07870.5990.24090.91156.5695-19.201223.1928
42.07070.8718-0.4623.3755-0.85143.2778-0.0951-0.1298-0.180.129-0.0191-0.0012-0.0040.10960.06610.30820.003-0.01130.36110.00930.308-17.7436-26.54833.1729
53.39550.87271.51722.6379-1.75093.4939-0.34990.6498-0.1088-0.1946-0.00830.58091.18580.2103-0.03520.5507-0.02810.01950.50630.02690.4478-16.6127-21.40087.3033
60.8049-0.79111.45632.0046-1.51148.64720.0531-0.0313-0.1465-0.5120.15720.16980.5232-0.1951-0.0670.5268-0.0573-0.01390.34860.01250.4867-21.4298-29.420119.5454
71.1785-0.39811.25432.3513-2.29623.7192-0.1707-0.1976-0.18-0.024-0.2845-0.35830.17760.43340.3980.33680.0647-0.04490.45740.04710.4323-6.7834-22.642831.0466
81.19220.2708-0.15851.2711-0.6862.82820.0037-0.0574-0.16510.0418-0.1279-0.2984-0.28180.62440.2920.4297-0.0333-0.00980.31140.00890.4449-8.9855-9.528521.4643
91.8465-1.68880.23292.2556-1.11845.5876-0.2927-0.188-0.0023-0.06110.15250.1559-0.5002-0.5662-0.04580.27280.0564-0.04380.38360.07560.403-29.625-11.087218.0246
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 171 )A147 - 171
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 228 )A172 - 228
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 249 )A229 - 249
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 286 )A250 - 286
7X-RAY DIFFRACTION7chain 'A' and (resid 287 through 343 )A287 - 343
8X-RAY DIFFRACTION8chain 'A' and (resid 344 through 397 )A344 - 397
9X-RAY DIFFRACTION9chain 'A' and (resid 398 through 436 )A398 - 436

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