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- PDB-7pvc: The structure of Kbp.K from E. coli with potassium bound. -

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Basic information

Entry
Database: PDB / ID: 7pvc
TitleThe structure of Kbp.K from E. coli with potassium bound.
ComponentsPotassium binding protein Kbp
KeywordsMETAL BINDING PROTEIN / potassium ion binding metal ion binding response to potassium ion response to stimulus cytoplasm
Function / homology
Function and homology information


response to potassium ion / potassium ion binding / cytoplasm
Similarity search - Function
Transport-associated and nodulation domain, bacteria / bacterial OsmY and nodulation domain / BON domain profile. / BON domain / BON domain / : / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain
Similarity search - Domain/homology
: / Potassium binding protein Kbp
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSmith, B.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: ACS Sens / Year: 2022
Title: Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies.
Authors: Torres Caban, C.C. / Yang, M. / Lai, C. / Yang, L. / Subach, F.V. / Smith, B.O. / Piatkevich, K.D. / Boyden, E.S.
#1: Journal: Structure / Year: 2016
Title: The Potassium Binding Protein Kbp Is a Cytoplasmic Potassium Sensor.
Authors: Ashraf, K.U. / Josts, I. / Mosbahi, K. / Kelly, S.M. / Byron, O. / Smith, B.O. / Walker, D.
History
DepositionOct 1, 2021Deposition site: PDBE / Processing site: PDBE
SupersessionOct 13, 2021ID: 5FIM
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.2Feb 16, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5Jun 15, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.6Oct 11, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium binding protein Kbp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1932
Polymers17,1541
Non-polymers391
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, NMR Distance Restraints, From inter-molecular 2J 13C=O...203/205Tl+ couplings observed in Kbp.Tl+ complex
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8320 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Potassium binding protein Kbp / K(+) binding protein Kbp


Mass: 17154.236 Da / Num. of mol.: 1 / Mutation: C-terminal His-tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: kbp, ygaU, yzzM, b2665, JW2640 / Plasmid: pKA1 / Details (production host): pET28 backbone / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ADE6
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D 1H-13C NOESY
141isotropic12D HBCBCGHD
151isotropic12D HBCBCGHE
161isotropic13D HBHA(CO)NH
171isotropic13D HBHANH
181isotropic13D H(CCO)NH
191isotropic13D (H)CCH-TOCSY
1101isotropic13D HN(CA)CB
1111isotropic13D HN(CA)CO
1121isotropic13D HNCO
1131isotropic13D (H)C(CCO)NH
1141isotropic12D 1H-15N HSQC
1151isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-13C; U-15N] Kbp, 20 mM sodium phosphate, 5 mM potassium chloride, 0.01 % sodium azide, 95% H2O/5% D2O
Label: CN.2 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMKbp[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
5 mMpotassium chloridenatural abundance1
0.01 %sodium azidenatural abundance1
Sample conditionsIonic strength: 25 mM / Label: CN.2 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2CCPNchemical shift assignment
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing2
simulated annealing3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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