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- PDB-8h5e: Crystal structure of the MgtE TM domain in complex with Ca2+ ions... -

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Basic information

Entry
Database: PDB / ID: 8h5e
TitleCrystal structure of the MgtE TM domain in complex with Ca2+ ions at 2.5 angstrom resolution
ComponentsMagnesium transporter MgtE
KeywordsTRANSPORT PROTEIN / Channels
Function / homology
Function and homology information


magnesium ion transmembrane transporter activity / metal ion binding / plasma membrane
Similarity search - Function
MgtE, N-terminal domain superfamily / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / Magnesium transporter MgtE / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily ...MgtE, N-terminal domain superfamily / SLC41A/MgtE, integral membrane domain / Magnesium transporter, MgtE intracellular domain / Magnesium transporter MgtE / SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily / Divalent cation transporter / MgtE intracellular N domain / MgtE intracellular N domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Magnesium transporter MgtE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTeng, X. / Sheng, D. / Hattori, M.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
National Natural Science Foundation of China (NSFC) China
CitationJournal: Iscience / Year: 2022
Title: Ion selectivity mechanism of the MgtE channel for Mg 2+ over Ca 2 .
Authors: Teng, X. / Sheng, D. / Wang, J. / Yu, Y. / Hattori, M.
History
DepositionOct 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 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: Magnesium transporter MgtE
B: Magnesium transporter MgtE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6939
Polymers39,4632
Non-polymers1,2307
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-67 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.760, 70.280, 103.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Magnesium transporter MgtE


Mass: 19731.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHB5018_11440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7R7TE27
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG 400, HEPES, NaSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40.54 Å / Num. obs: 17028 / % possible obs: 99.9 % / Redundancy: 35.3 % / CC1/2: 0.995 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.65 Å / Num. unique obs: 2665 / CC1/2: 0.574

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u9l

4u9l


Resolution: 2.5→40.54 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 1686 9.93 %
Rwork0.2326 --
obs0.2353 16972 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2671 0 65 91 2827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052781
X-RAY DIFFRACTIONf_angle_d1.1943789
X-RAY DIFFRACTIONf_dihedral_angle_d21.273422
X-RAY DIFFRACTIONf_chiral_restr0.067487
X-RAY DIFFRACTIONf_plane_restr0.006451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.3661220.30721255X-RAY DIFFRACTION100
2.57-2.660.29481510.2951243X-RAY DIFFRACTION100
2.66-2.750.30991300.28511237X-RAY DIFFRACTION100
2.75-2.860.31421470.2691260X-RAY DIFFRACTION100
2.86-2.990.2891410.26541261X-RAY DIFFRACTION100
2.99-3.150.28121400.24891251X-RAY DIFFRACTION100
3.15-3.350.28461340.24271279X-RAY DIFFRACTION100
3.35-3.610.26381440.2331267X-RAY DIFFRACTION100
3.61-3.970.26361420.2151272X-RAY DIFFRACTION100
3.97-4.540.26131420.23231288X-RAY DIFFRACTION100
4.54-5.710.24581410.22911296X-RAY DIFFRACTION100
5.72-40.540.22161520.20591377X-RAY DIFFRACTION100

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