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- PDB-7aht: Structure of the N-domain of the K+/H+ antiporter subunit KhtT at... -

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Basic information

Entry
Database: PDB / ID: 7aht
TitleStructure of the N-domain of the K+/H+ antiporter subunit KhtT at pH 7.5
ComponentsK(+)/H(+) antiporter subunit KhtT
KeywordsTRANSPORT PROTEIN / Regulatory protein of K+/H+ antiporter
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / plasma membrane
Similarity search - Function
Potassium/proton antiporter subunit KhtT / : / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile.
Similarity search - Domain/homology
K(+)/H(+) antiporter subunit KhtT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsCereija, T.B. / Morais-Cabral, J.H.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-029863(PTDC/BIA-BQM/29863/2017) Portugal
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: c-di-AMP, a likely master regulator of bacterial K + homeostasis machinery, activates a K + exporter.
Authors: Cereija, T.B. / Guerra, J.P.L. / Jorge, J.M.P. / Morais-Cabral, J.H.
History
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 14, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K(+)/H(+) antiporter subunit KhtT
B: K(+)/H(+) antiporter subunit KhtT


Theoretical massNumber of molelcules
Total (without water)16,0142
Polymers16,0142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-18 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.524, 48.524, 66.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein K(+)/H(+) antiporter subunit KhtT


Mass: 8006.892 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: khtT, yhaT, BSU09860 / Production host: Escherichia coli (E. coli) / References: UniProt: O07535

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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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 7.5 1.6 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978566 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978566 Å / Relative weight: 1
ReflectionResolution: 2.16→48.52 Å / Num. obs: 8366 / % possible obs: 99.8 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.014 / Rrim(I) all: 0.05 / Net I/σ(I): 22.4
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.207 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 734 / CC1/2: 0.943 / Rpim(I) all: 0.333 / Rrim(I) all: 1.252 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AGV

7agv


Resolution: 2.16→34.312 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 47.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 444 5.36 %
Rwork0.2448 7842 -
obs0.2468 8286 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.58 Å2 / Biso mean: 91.5133 Å2 / Biso min: 46.07 Å2
Refinement stepCycle: final / Resolution: 2.16→34.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 0 0 980
Num. residues----123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002987
X-RAY DIFFRACTIONf_angle_d0.5011317
X-RAY DIFFRACTIONf_chiral_restr0.038146
X-RAY DIFFRACTIONf_plane_restr0.001175
X-RAY DIFFRACTIONf_dihedral_angle_d11.551388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1601-2.47250.35111570.3054256799
2.4725-3.11480.39741170.36082650100
3.1148-34.3120.25911700.2184262599
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)
16.2631-2.2603-1.32443.4866-3.08679.4775-0.23671.1146-0.7635-1.81590.3302-0.20150.6484-0.6549-0.06180.6559-0.13230.02220.7556-0.02460.479421.47187.3585-6.655
25.19793.43372.7575.3302-0.78683.4127-0.7826-0.6011-0.2369-1.20120.5703-0.4044-1.66230.53560.26520.8995-0.1181-0.02350.8005-0.11160.465120.659211.88092.0703
34.1899-0.8271-1.66630.2143-0.46261.60170.1111-2.0992-0.86620.6401-0.01780.6055-0.7897-1.6047-0.2861.01050.0070.08481.0751-0.05150.706512.12529.57914.1367
49.1959-2.03912.9772.4491-1.16353.0986-0.0176-0.81190.5670.3134-0.0438-0.6551-1.13251.06640.17560.7044-0.1243-0.10050.89390.02230.57627.81552.59668.9987
58.87355.0906-1.17074.8715-4.8048.16640.7205-1.21840.37842.6682-0.63211.23270.0259-0.35530.11050.88330.04620.0090.7171-0.07140.64722.0072-4.868418.3241
64.9920.7018-0.69474.0358-4.64796.7854-0.3298-0.29760.63621.93140.69280.8702-1.2085-0.7644-0.29650.90270.16480.05681.0628-0.07520.442218.9513-0.623415.0389
74.6337-0.3112-0.09197.2751-5.88534.6230.22570.6218-0.5257-1.01130.03880.34781.45-1.3118-0.36820.8234-0.053-0.07380.8780.01680.411417.4732-7.0687.7506
86.5497-3.8753-5.68753.33572.99484.96330.4471.4116-0.8467-2.1211-0.92461.9912-0.25340.19650.57411.1995-0.1101-0.11651.0470.09620.681414.0362-2.50523.0747
93.76224.1991-1.17858.60590.06492.7401-0.68561.1829-0.5109-2.78380.7489-0.33582.15991.2991-0.15861.132-0.03690.0580.9421-0.00870.480426.6837-1.4866-0.9068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 30 )A0 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 40 )A31 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 55 )A41 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 68 )A56 - 68
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 8 )B1 - 8
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 23 )B9 - 23
7X-RAY DIFFRACTION7chain 'B' and (resid 24 through 38 )B24 - 38
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 55 )B39 - 55
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 68 )B56 - 68

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