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

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Basic information

Entry
Database: PDB / ID: 7agw
TitleStructure of the N-domain of the K+/H+ antiporter subunit KhtT at pH 6.5
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: 1.511 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 23, 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
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-18 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.700, 62.982, 65.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris propane pH 6.5 200 mM Ammonium sulfate 35% PEG MME 2000

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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: 1.51→45.33 Å / Num. obs: 23010 / % possible obs: 99.5 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.013 / Rrim(I) all: 0.046 / Net I/σ(I): 23.1
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.459 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1055 / CC1/2: 0.786 / Rpim(I) all: 0.43 / Rrim(I) all: 1.524 / % possible all: 93.5

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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: 1.511→30.642 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 1118 4.88 %
Rwork0.2221 21779 -
obs0.2233 22897 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.6 Å2 / Biso mean: 46.6779 Å2 / Biso min: 23.4 Å2
Refinement stepCycle: final / Resolution: 1.511→30.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 75 1189
Biso mean---48.97 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061198
X-RAY DIFFRACTIONf_angle_d0.9581619
X-RAY DIFFRACTIONf_chiral_restr0.068174
X-RAY DIFFRACTIONf_plane_restr0.003225
X-RAY DIFFRACTIONf_dihedral_angle_d13.77479
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5114-1.58020.41011240.3812260397
1.5802-1.66350.34091350.3228268599
1.6635-1.76770.31891370.27982697100
1.7677-1.90410.27991310.2332717100
1.9041-2.09570.24241360.2146269899
2.0957-2.39890.25411530.22232737100
2.3989-3.02190.25881690.24522750100
3.0219-30.6420.21751330.1993289299
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)
14.72941.4468-0.98753.6598-5.20268.4830.1205-0.34510.01510.81410.13080.4615-0.08340.2009-0.22690.38630.03380.05920.2661-0.020.2439-6.69267.140328.258
27.68321.86890.18763.4629-1.53157.88670.1105-0.6811-1.20770.88790.1298-0.20140.86010.4521-0.10480.4360.113-0.02850.28560.05330.3728-3.00770.394324.3018
34.9731-0.72370.16472.8733.05843.3708-0.21830.53180.36710.17460.12950.016-0.9349-0.18620.05750.32770.05390.00120.26980.0210.2616-3.07987.705817.9349
47.78173.9704-6.41843.4165-3.26775.3016-0.6849-0.2408-2.0298-0.1193-1.0037-1.55910.38341.21480.49631.02820.1937-0.370.7007-0.08541.124410.0589-0.36927.5072
56.199-6.13355.64456.4316-5.50875.1862-0.6619-0.30521.090.02820.3871-1.2174-0.6947-0.11420.23340.2673-0.0271-0.00820.395-0.08620.381.28334.378614.6391
67.75224.05390.25933.0518-0.92383.1912-0.24180.33250.0127-1.15060.14210.5532-0.3357-0.66450.02170.35790.0906-0.07050.3715-0.04460.3031-11.85020.43411.0842
73.497-2.62571.33094.2764-3.42054.05590.26160.19290.04-2.34880.03270.76560.70640.0387-0.01830.66190.0149-0.0620.2621-0.01820.3031-6.226-6.45921.7714
84.19531.6195-2.13973.139-2.92297.52010.15970.07480.2141-0.71780.0190.0664-0.17080.3253-0.13120.3034-0.017-0.02560.26030.02140.2264-3.5992-5.39225.5706
97.1934-0.75010.11679.76362.92156.8724-0.0526-0.12250.1014-0.3570.3543-0.60990.14450.3672-0.18810.24620.0168-0.01520.2324-0.02050.19360.6354-8.190812.921
107.4033-4.06470.06025.0821-2.35383.338-0.7016-0.2941-0.41121.32730.7841.04190.3036-1.3285-0.18640.4246-0.04120.11250.4952-0.02250.3507-11.9732-3.798221.4447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )A0 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 30 )A19 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 40 )A31 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 47 )A41 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 55 )A48 - 55
6X-RAY DIFFRACTION6chain 'A' and (resid 56 through 68 )A56 - 68
7X-RAY DIFFRACTION7chain 'B' and (resid -2 through 8 )B-2 - 8
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 23 )B9 - 23
9X-RAY DIFFRACTION9chain 'B' and (resid 24 through 55 )B24 - 55
10X-RAY DIFFRACTION10chain 'B' and (resid 56 through 68 )B56 - 68

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