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- PDB-2jvi: NMR Solution Structure of the Hyper-Sporulation Response Regulato... -

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Basic information

Entry
Database: PDB / ID: 2jvi
TitleNMR Solution Structure of the Hyper-Sporulation Response Regulator Spo0F Mutant H101A from Bacillus subtilis
ComponentsSporulation initiation phosphotransferase F
KeywordsTRANSFERASE / RESPONSE REGULATOR / TWO-COMPONENT SYSTEMS / BACTERIAL SIGNAL TRANSDUCTION / PHOSPHO-RELAY / (BETA/ALPHA)5 PROTEIN / Cytoplasm / Kinase / Magnesium / Metal-binding / Phosphorylation / Sporulation / Two-component regulatory system
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / sporulation resulting in formation of a cellular spore / phosphorelay signal transduction system / kinase activity / phosphorylation / metal ion binding / cytoplasm
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sporulation initiation phosphotransferase F
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBobay, B.G. / McLaughlin, P.D. / Thompson, R.J. / Hoch, J.A. / Cavanagh, J.
CitationJournal: To be Published
Title: Covariance identifies dynamic residues at the interfaces in protein/protein complexes
Authors: Bobay, B.G. / White, R.A. / Szurmant, H. / Sullivan, D.M. / McLaughlin, P.D. / Hwa, T. / Hoch, J.A. / Cavanagh, J.
History
DepositionSep 20, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sporulation initiation phosphotransferase F


Theoretical massNumber of molelcules
Total (without water)15,2491
Polymers15,2491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sporulation initiation phosphotransferase F / Stage 0 sporulation protein F


Mass: 15248.745 Da / Num. of mol.: 1 / Mutation: H101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spo0F / Plasmid: pET-20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE)3
References: UniProt: P06628, Transferases; Transferring phosphorus-containing groups

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Spo0F Mutant H101A
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HN(CA)CO
1713D HNCA
1813D HN(CO)CA
1923D (H)CCH-TOCSY
11013D 1H-15N TOCSY
11113D 1H-15N NOESY
11223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM TRIS, 50 mM potassium chloride, 0.02 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
225 mM TRIS, 50 mM potassium chloride, 0.02 % sodium azide, 1 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMTRIS1
50 mMpotassium chloride1
0.02 %sodium azide1
1 mMentity[U-100% 13C; U-100% 15N]1
25 mMTRIS2
50 mMpotassium chloride2
0.02 %sodium azide2
1 mMentity[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 25 / pH: 6.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5Johnson, One Moon Scientificdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2640 / NOE intraresidue total count: 665 / NOE medium range total count: 1470 / NOE sequential total count: 1975
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 1.8 Å / Maximum upper distance constraint violation: 6 Å
NMR ensemble rmsDistance rms dev: 0.046 Å / Distance rms dev error: 0.001 Å

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