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- PDB-1pv0: Structure of the Sda antikinase -

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Basic information

Entry
Database: PDB / ID: 1pv0
TitleStructure of the Sda antikinase
ComponentsSda
KeywordsSIGNALING PROTEIN / Sda / KinA / antikinase / histidine kinase / sporulation phosphorelay
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / protein kinase inhibitor activity
Similarity search - Function
Sporulation inhibitor A / Sporulation inhibitor A / Sporulation inhibitor A superfamily / Sporulation inhibitor A / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sporulation inhibitor sda
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsRowland, S.L. / Burkholder, W.F. / Maciejewski, M.W. / Grossman, A.D. / King, G.F.
Citation
Journal: Mol.Cell / Year: 2004
Title: Structure and mechanism of Sda: an inhibitor of the histidine kinases that regulate initiation of sporulation in Bacillus subtilis
Authors: Rowland, S.L. / Burkholder, W.F. / Cunningham, K.A. / Maciejewski, M.W. / Grossman, A.D. / King, G.F.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Replication initiation proteins regulate a developmental checkpoint in Bacillus subtilis
Authors: Burkholder, W.F. / Kurster, I. / Grossman, A.D.
History
DepositionJun 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 999SEQUENCE The sequence of this protein is not available in any reference sequence database

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sda


Theoretical massNumber of molelcules
Total (without water)5,4481
Polymers5,4481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50Structures with lowest energy and least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Sda


Mass: 5448.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: sda / Plasmid: pSLR65 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lambda DE3) / References: UniProt: Q7WY62

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HC(CO)NH-TOCSY
1613D C(CO)NH-TOCSY
171HNHA
1813D HNHB
2923D 13C-separated NOESY
21023D (H)CCH-COSY
21122D DQF-COSY
21222D TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Sda, 20 mM sodium phosphate, 100 mM NaCl, H2OH2O
21 mM Sda, 20 mM sodium phosphate, 100 mM NaCl, D2OD2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11606.851 atm298 K
21606.851 atm298 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
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Frank Delagliodata analysis
DYANA1.5Peter Guentertstructure solution
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Structures with lowest energy and least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 25

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