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- PDB-5x9h: Crystal structure of the Mg2+ channel MgtE in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 5x9h
TitleCrystal structure of the Mg2+ channel MgtE in complex with ATP
ComponentsMagnesium transporter MgtE
KeywordsMETAL TRANSPORT / channels
Function / homology
Function and homology information


magnesium ion transport / magnesium ion transmembrane transporter activity / magnesium ion binding / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
SLC41 divalent cation transporters, integral membrane domain / MgtE N-terminal fold / MgtE N-terminal domain-like / 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 ...SLC41 divalent cation transporters, integral membrane domain / MgtE N-terminal fold / MgtE N-terminal domain-like / 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 / CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Tetracycline Repressor; domain 2 / CBS domain / CBS domain / CBS domain profile. / Alpha Horseshoe / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Magnesium transporter MgtE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.598 Å
AuthorsTomita, A. / Hattori, M. / Nureki, O.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0502800 China
CitationJournal: Nat Commun / Year: 2017
Title: ATP-dependent modulation of MgtE in Mg(2+) homeostasis
Authors: Tomita, A. / Zhang, M. / Jin, F. / Zhuang, W. / Takeda, H. / Maruyama, T. / Osawa, M. / Hashimoto, K.I. / Kawasaki, H. / Ito, K. / Dohmae, N. / Ishitani, R. / Shimada, I. / Yan, Z. / Hattori, M. / Nureki, O.
History
DepositionMar 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)106,31317
Polymers104,9832
Non-polymers1,33015
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-57 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.330, 85.651, 156.558
Angle α, β, γ (deg.)90.00, 100.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Magnesium transporter MgtE


Mass: 52491.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1060 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SMG8
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg

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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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 9% PEG 4000, 0.2 M MgCl2, and 0.05 M MES pH 6.5, 10 mM ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.598→50.329 Å / Num. obs: 20361 / % possible obs: 98.5 % / Redundancy: 6.8 % / Net I/σ(I): 15.09

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.598→50.329 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.8
RfactorNum. reflection% reflection
Rfree0.2832 1993 9.79 %
Rwork0.2501 --
obs0.2533 20361 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.598→50.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6447 0 75 0 6522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016633
X-RAY DIFFRACTIONf_angle_d1.5199116
X-RAY DIFFRACTIONf_dihedral_angle_d20.2532334
X-RAY DIFFRACTIONf_chiral_restr0.0551143
X-RAY DIFFRACTIONf_plane_restr0.0091140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5985-3.68840.45651420.38641309X-RAY DIFFRACTION98
3.6884-3.78810.37621410.33561299X-RAY DIFFRACTION98
3.7881-3.89950.34181380.28821281X-RAY DIFFRACTION97
3.8995-4.02540.27551440.26681323X-RAY DIFFRACTION99
4.0254-4.16920.32111400.25051288X-RAY DIFFRACTION98
4.1692-4.3360.29651410.24221302X-RAY DIFFRACTION99
4.336-4.53320.2811440.21231323X-RAY DIFFRACTION99
4.5332-4.7720.23661400.20261313X-RAY DIFFRACTION99
4.772-5.07080.25261410.19111296X-RAY DIFFRACTION97
5.0708-5.46180.22551410.19731298X-RAY DIFFRACTION98
5.4618-6.01070.28151450.24071327X-RAY DIFFRACTION99
6.0107-6.87860.33651450.25851333X-RAY DIFFRACTION99
6.8786-8.65910.24821430.26321317X-RAY DIFFRACTION98
8.6591-50.33380.28441480.26511359X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 6.7213 Å / Origin y: -1.8839 Å / Origin z: 183.013 Å
111213212223313233
T1.1842 Å20.1402 Å20.0127 Å2-1.0152 Å20.0608 Å2--0.9482 Å2
L3.2197 °20.3449 °20.7327 °2-0.6909 °2-0.4347 °2--4.7956 °2
S0.1294 Å °-1.0625 Å °-0.4493 Å °0.0929 Å °0.0028 Å °0.1742 Å °0.7181 Å °-0.1538 Å °-0.164 Å °
Refinement TLS groupSelection details: all

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