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- PDB-8gpv: Cytoplasmic domain structure of the MgtE Mg2+ channel from Clostr... -

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Basic information

Entry
Database: PDB / ID: 8gpv
TitleCytoplasmic domain structure of the MgtE Mg2+ channel from Clostridiales bacterium
ComponentsMagnesium transporter MgtE
KeywordsTRANSPORT PROTEIN / ion 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
Magnesium transporter MgtE
Similarity search - Component
Biological speciesClostridiales bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWang, M. / Zhao, Y. / Hattori, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071234 China
Ministry of Science and Technology (MoST, China)2016YFA0502800 China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2023
Title: Novel Mg 2+ binding sites in the cytoplasmic domain of the MgtE Mg 2+ channels revealed by X-ray crystal structures.
Authors: Wang, M. / Zhao, Y. / Hayashi, Y. / Ito, K. / Hattori, M.
History
DepositionAug 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 31, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1118
Polymers28,7271
Non-polymers3847
Water3,927218
1
A: Magnesium transporter MgtE
hetero molecules

A: Magnesium transporter MgtE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,22116
Polymers57,4532
Non-polymers76814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area4630 Å2
ΔGint-100 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.063, 81.063, 104.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

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Components

#1: Protein Magnesium transporter MgtE


Mass: 28726.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridiales bacterium (bacteria) / Gene: mgtE, DGR79_01085 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3D5MLJ3
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M sodium chloride, 0.1 M MOPS pH 7.5, 38% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.82→81.06 Å / Num. obs: 28748 / % possible obs: 89.3 % / Redundancy: 25 % / CC1/2: 1 / Net I/σ(I): 38.1
Reflection shellResolution: 1.82→1.91 Å / Num. unique obs: 4197 / CC1/2: 0.877

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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: 2YVY

2yvy


Resolution: 1.82→81.06 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 1473 5.12 %
Rwork0.2246 --
obs0.2263 28748 89.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→81.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 25 212 2186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081999
X-RAY DIFFRACTIONf_angle_d1.0632736
X-RAY DIFFRACTIONf_dihedral_angle_d17.192286
X-RAY DIFFRACTIONf_chiral_restr0.059329
X-RAY DIFFRACTIONf_plane_restr0.006356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.35761600.31152690X-RAY DIFFRACTION100
1.87-1.940.39071060.3081868X-RAY DIFFRACTION69
1.94-2.020.37841290.27212739X-RAY DIFFRACTION100
2.02-2.110.29631220.2772066X-RAY DIFFRACTION76
2.11-2.220.3111370.27112754X-RAY DIFFRACTION100
2.22-2.360.32281200.27312019X-RAY DIFFRACTION74
2.36-2.540.34511540.26932768X-RAY DIFFRACTION100
2.54-2.80.33761190.27162288X-RAY DIFFRACTION82
2.8-3.20.27891490.24542780X-RAY DIFFRACTION100
3.2-4.040.25141330.20942303X-RAY DIFFRACTION81
4.04-81.060.19961440.19193000X-RAY DIFFRACTION99

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