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- PDB-2a29: The solution structure of the AMP-PNP bound nucleotide binding do... -

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Basic information

Entry
Database: PDB / ID: 2a29
TitleThe solution structure of the AMP-PNP bound 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Potassium-transporting ATPase ATP-binding subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsHaupt, M. / Bramkamp, M. / Coles, M. / Altendorf, K. / Kessler, H.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Holo-form of the Nucleotide Binding Domain of the KdpFABC Complex from Escherichia coli Reveals a New Binding Mode
Authors: Haupt, M. / Bramkamp, M. / Heller, M. / Coles, M. / Deckers-Hebestreit, G. / Herkenhoff-Hesselmann, B. / Altendorf, K. / Kessler, H.
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: PDBJ
SupersessionDec 20, 2005ID: 1X6K
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6742
Polymers17,1681
Non-polymers5061
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein Potassium-transporting ATPase B chain / potassium-transporting P-type ATPase / KdpFABC / ATP phosphohydrolase [potassium- transporting] B ...potassium-transporting P-type ATPase / KdpFABC / ATP phosphohydrolase [potassium- transporting] B chain / Potassium binding and translocating subunit B


Mass: 17168.297 Da / Num. of mol.: 1 / Fragment: KdpBN, nucleotide binding domain of KdpB
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
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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

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Sample preparation

DetailsContents: 1.0MM U-15N, 13C KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE, 15MM ATP- PNP; 1.0MM U-15N KDPBN, 50MM PHOSPHATE BUFFER, 100MM NACL, 0.05% SODIUM AZIDE, 15MM AMP- PNP
Sample conditionsIonic strength: 100mM NACL / pH: 6.0 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

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
XwinNMR3.5Brukerstructure solution
X-PLORNIH-2.9.3Brungerstructure solution
Sparky3.11Goddard, Knellerdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: BASED ON A TOTAL OF 1667 NOE-BASED DISTANCE RESTRAINTS, 230 DIHEDRAL ANGLE RESTRAINTS AND 21 INTERMOLECULAR DISTANCE RESTRAINTS
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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