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- PDB-3l9x: KefC C-terminal domain in complex with KefF and ESG -

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Basic information

Entry
Database: PDB / ID: 3l9x
TitleKefC C-terminal domain in complex with KefF and ESG
ComponentsGlutathione-regulated potassium-efflux system protein kefC, linker, ancillary protein kefF
KeywordsTRANSPORT PROTEIN / potassium channel regulation / potassium efflux / glutathione / KTN(RCK) domains
Function / homology
Function and homology information


glutathione-regulated potassium exporter activity / response to methylglyoxal / potassium:proton antiporter complex / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / intracellular pH elevation / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / regulation of pH / positive regulation of potassium ion transmembrane transport ...glutathione-regulated potassium exporter activity / response to methylglyoxal / potassium:proton antiporter complex / NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / intracellular pH elevation / NADH:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / regulation of pH / positive regulation of potassium ion transmembrane transport / antiporter activity / toxic substance binding / proton transmembrane transport / regulation of intracellular pH / potassium ion transport / response to hydrogen peroxide / response to toxic substance / FMN binding / electron transfer activity / nucleotide binding / enzyme binding / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Glutathione-regulated potassium-efflux system ancillary protein KefF / : / Glutathione-regulated potassium-efflux system protein KefC / K+/H+ exchanger / Potassium uptake protein TrkA / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Regulator of K+ conductance, N-terminal / TrkA-N domain ...Glutathione-regulated potassium-efflux system ancillary protein KefF / : / Glutathione-regulated potassium-efflux system protein KefC / K+/H+ exchanger / Potassium uptake protein TrkA / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger family / Regulator of K+ conductance, N-terminal / TrkA-N domain / Flavodoxin-like fold / Flavodoxin-like fold / RCK N-terminal domain profile. / Flavodoxin domain / Flavoprotein-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ESG / FLAVIN MONONUCLEOTIDE / Chem-L9X / Glutathione-regulated potassium-efflux system protein KefC / Glutathione-regulated potassium-efflux system ancillary protein KefF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRoosild, T.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism of ligand-gated potassium efflux in bacterial pathogens.
Authors: Roosild, T.P. / Castronovo, S. / Healy, J. / Miller, S. / Pliotas, C. / Rasmussen, T. / Bartlett, W. / Conway, S.J. / Booth, I.R.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione-regulated potassium-efflux system protein kefC, linker, ancillary protein kefF
B: Glutathione-regulated potassium-efflux system protein kefC, linker, ancillary protein kefF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,21610
Polymers93,1162
Non-polymers2,1018
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-181 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.949, 85.941, 189.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 1147 - 1159 / Label seq-ID: 384 - 396

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutathione-regulated potassium-efflux system protein kefC, linker, ancillary protein kefF / K(+)/H(+) antiporter


Mass: 46557.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0047, JW0046, kefC, trkC, b0046, JW0045, kefF, yabF / Plasmid: pHis8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03819, UniProt: P0A754

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Non-polymers , 6 types, 252 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ESG / L-gamma-glutamyl-S-[(3S)-1-ethyl-2,5-dioxopyrrolidin-3-yl]-L-cysteinylglycine


Mass: 432.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N4O8S
#6: Chemical ChemComp-L9X / L-gamma-glutamyl-S-[(3R)-1-ethyl-2,5-dioxopyrrolidin-3-yl]-L-cysteinylglycine


Mass: 432.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N4O8S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 9% PEG 3350, 100mM ammonium sulfate, 100mM Bis-Tris buffer, 50mM magnesium formate, 1mM NAD+, pH 5.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 62001 / % possible obs: 98.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / % possible all: 91

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EYW

3eyw


Resolution: 2.1→38.26 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.164 / SU ML: 0.111 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23567 3110 5 %RANDOM
Rwork0.20281 ---
obs0.20445 58735 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.692 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--1.85 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 132 244 5774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215653
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9647668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60423.162272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.115932
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6661542
X-RAY DIFFRACTIONr_chiral_restr0.0970.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024330
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22396
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23733
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1131.53467
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71425342
X-RAY DIFFRACTIONr_scbond_it2.58132613
X-RAY DIFFRACTIONr_scangle_it3.9674.52326
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
52medium positional0.110.5
48loose positional0.475
52medium thermal2.992
48loose thermal4.0910
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 206 -
Rwork0.248 3921 -
obs--89.93 %

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