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- PDB-1u7q: THE SOLUTION STRUCTURE OF THE NUCLEOTIDE BINDING DOMAIN OF KDPB -

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Basic information

Entry
Database: PDB / ID: 1u7q
TitleTHE SOLUTION STRUCTURE OF THE NUCLEOTIDE BINDING DOMAIN OF KDPB
ComponentsPotassium-transporting ATPase B chain
KeywordsHYDROLASE / ALPHA-BETA SANDWICH
Function / homology
Function and homology information


P-type K+ transporter / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / P-type potassium transmembrane transporter activity / monoatomic cation transmembrane transport / potassium ion transmembrane transport / potassium ion transport / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
P-type ATPase, B chain, subfamily IA / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase ...P-type ATPase, B chain, subfamily IA / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Potassium-transporting ATPase ATP-binding subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsHaupt, M. / Bramkamp, M. / Coles, M. / Altendorf, K. / Kessler, H.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Inter-domain motions of the N-domain of the KdpFABC complex, a P-type ATPase, are not driven by ATP-induced conformational changes.
Authors: Haupt, M. / Bramkamp, M. / Coles, M. / Altendorf, K. / Kessler, H.
History
DepositionAug 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: 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-transporting ATPase B chain


Theoretical massNumber of molelcules
Total (without water)17,1681
Polymers17,1681
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Potassium-transporting ATPase B chain / Potassium-translocating ATPase B chain / ATP phosphohydrolase [potassium-transporting] B chain / ...Potassium-translocating ATPase B chain / ATP phosphohydrolase [potassium-transporting] B chain / Potassium binding and translocating subunit B / KDPB N-domain / KdpBN / Kdp B chain N-domain


Mass: 17168.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdpB / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03960, EC: 3.6.3.12

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
121CNH- NOESY
NMR detailsText: FEWEST VIOLATIONS

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Sample preparation

DetailsContents: 1.4MM U-15N,13C KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE; 1.2MM U-15N KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE
Sample conditionsIonic strength: 100mM NACL / pH: 6.0 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX9001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIH-2.9.3BRUNGERrefinement
XwinNMR3.5structure solution
X-PLORNIH-2.9.3structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: BASED ON A TOTAL OF 2232 NOE-BASED DISTANCE RESTRAINTS, 256 DIHEDRAL ANGLE RESTRAINTS, 67 J-RESTRAINTS AND 66 HYDROGEN BOND RESTRAINTS
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 20

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