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- PDB-8gps: Cytoplasmic domain structure of the MgtE Mg2+ channel from Chryse... -

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Basic information

Entry
Database: PDB / ID: 8gps
TitleCytoplasmic domain structure of the MgtE Mg2+ channel from Chryseobacterium hispalense
ComponentsMgtE
KeywordsTRANSPORT PROTEIN / ion channels
Biological speciesChryseobacterium hispalense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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

Downloads & links

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Assembly

Deposited unit
A: MgtE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0916
Polymers27,9701
Non-polymers1225
Water4,161231
1
A: MgtE
hetero molecules

A: MgtE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,18212
Polymers55,9392
Non-polymers24310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3770 Å2
ΔGint-100 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.503, 57.503, 118.252
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

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Components

#1: Protein MgtE


Mass: 27969.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium hispalense (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1 M sodium chloride, 0.1 M magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 20% v/v pentaerythritol

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→49.8 Å / Num. obs: 46278 / % possible obs: 99.9 % / Redundancy: 18 % / CC1/2: 0.99 / Net I/σ(I): 20.4
Reflection shellResolution: 1.39→1.46 Å / Num. unique obs: 6708 / CC1/2: 0.963

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YVY

2yvy


Resolution: 1.39→25.86 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2316 2379 5.14 %
Rwork0.1838 --
obs0.1862 46278 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 5 231 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061914
X-RAY DIFFRACTIONf_angle_d0.862642
X-RAY DIFFRACTIONf_dihedral_angle_d11.625284
X-RAY DIFFRACTIONf_chiral_restr0.081323
X-RAY DIFFRACTIONf_plane_restr0.007341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.34861160.33442568X-RAY DIFFRACTION99
1.42-1.450.38381650.29892514X-RAY DIFFRACTION99
1.45-1.480.32521020.26252554X-RAY DIFFRACTION99
1.48-1.520.2821450.2342550X-RAY DIFFRACTION99
1.52-1.560.26551590.20742511X-RAY DIFFRACTION99
1.56-1.610.21881160.20072566X-RAY DIFFRACTION99
1.61-1.660.23121180.19482562X-RAY DIFFRACTION99
1.66-1.720.23111840.1862498X-RAY DIFFRACTION99
1.72-1.790.21131550.18772540X-RAY DIFFRACTION100
1.79-1.870.26351480.18862566X-RAY DIFFRACTION100
1.87-1.970.24591230.18312601X-RAY DIFFRACTION100
1.97-2.090.22621420.18562575X-RAY DIFFRACTION100
2.09-2.250.24861370.17512596X-RAY DIFFRACTION100
2.25-2.480.21171210.22620X-RAY DIFFRACTION100
2.48-2.830.2441630.19642606X-RAY DIFFRACTION100
2.83-3.570.2621350.18262690X-RAY DIFFRACTION100
3.57-25.860.19711500.15982782X-RAY DIFFRACTION100

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