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- PDB-1buz: SOLUTION STRUCTURE OF SPOIIAA, A PHOSPHORYLATABLE COMPONENT OF TH... -

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Basic information

Entry
Database: PDB / ID: 1buz
TitleSOLUTION STRUCTURE OF SPOIIAA, A PHOSPHORYLATABLE COMPONENT OF THE SYSTEM THAT REGULATES TRANSCRIPTION FACTOR SIGMA-F OF BACILLUS SUBTILIS NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsSPOIIAA
KeywordsTRANSCRIPTION REGULATOR / KINASE SUBSTRATE / ANTI-ANTI SIGMA FACTOR / NOVEL ALPHA/BETA FOLD / SPORULATION / PHOSPHORYLATION
Function / homology
Function and homology information


anti-sigma factor antagonist activity / antisigma factor binding / sporulation resulting in formation of a cellular spore
Similarity search - Function
Anti-sigma F factor antagonist / Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Anti-sigma F factor antagonist
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKovacs, H. / Comfort, D. / Lord, M. / Campbell, I.D. / Yudkin, M.D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Solution structure of SpoIIAA, a phosphorylatable component of the system that regulates transcription factor sigmaF of Bacillus subtilis.
Authors: Kovacs, H. / Comfort, D. / Lord, M. / Campbell, I.D. / Yudkin, M.D.
#1: Journal: Science / Year: 1995
Title: Activation of Cell-Specific Transcription by a Serine Phosphatase at the Site of Asymmetric Division
Authors: Duncan, L. / Alper, S. / Arigoni, F. / Losick, R. / Stragier, P.
#2: Journal: Genes Dev. / Year: 1994
Title: Role of Interactions between Spoiiaa and Spoiiab in Regulating Cell-Specific Transcription Factor Sigma F of Bacillus Subtilis
Authors: Diederich, B. / Wilkinson, J.F. / Magnin, T. / Najafi, S.M.A. / Errington, J. / Yudkin, M.D.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1994
Title: An Adenosine Nucleotide Switch Controlling the Activity of a Cell Type-Specific Transcription Factor in B. Subtilis
Authors: Alper, S. / Duncan, L. / Losick, R.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1993
Title: Sigma F, the First Compartment-Specific Transcription Factor of B. Subtilis, is Regulated by an Anti-Sigma Factor that is Also a Protein Kinase
Authors: Min, K.T. / Hilditch, C.M. / Diederich, B. / Errington, J. / Yudkin, M.D.
#5: Journal: J.Bacteriol. / Year: 1993
Title: Molecular and Phenotypic Characterization of Promoter-Proximal Mutations in the Spoiia Locus of Bacillus Subtilis
Authors: Challoner-Courtney, I.J. / Yudkin, M.D.
History
DepositionSep 8, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 8, 2018Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_nmr_details ...entity_src_gen / pdbx_nmr_details / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _entity_src_gen.gene_src_genus / _entity_src_gen.host_org_genus ..._entity_src_gen.gene_src_genus / _entity_src_gen.host_org_genus / _entity_src_gen.host_org_species / _entity_src_gen.pdbx_host_org_strain / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_refine.method / _pdbx_nmr_software.authors / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.manufacturer
Revision 1.5Apr 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPOIIAA


Theoretical massNumber of molelcules
Total (without water)12,8751
Polymers12,8751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100TARGET FUNCTION AND LEAST RESTRAINT VIOLATIONS
RepresentativeModel #1target function and least restraint violations

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Components

#1: Protein SPOIIAA


Mass: 12874.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NON-PHOSPHORYLATED FORM / Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: SG38 / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: SPOIIAA / Plasmid: PEAA / Cellular location (production host): CYTOPLASM / Gene (production host): SPOIIAA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P10727

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131HSQC
141HMQC-J
151HNCA
161CBCA(CO)NH
171HBHA(CO)NH
NMR detailsText: SEQUENTIAL ASSIGNMENT WAS OBTAINED BY ANALYSIS OF HNCA, CBCA(CO)NH, HAHB(CO)NH AND 15N- CORRELATED NOESY SPECTRA. DISTANCE CONSTRAINTS WERE COLLECTED FROM NOESY SPECTRA IN H2O AND D2O AND A 15N- ...Text: SEQUENTIAL ASSIGNMENT WAS OBTAINED BY ANALYSIS OF HNCA, CBCA(CO)NH, HAHB(CO)NH AND 15N- CORRELATED NOESY SPECTRA. DISTANCE CONSTRAINTS WERE COLLECTED FROM NOESY SPECTRA IN H2O AND D2O AND A 15N- CORRELATED NOESY SPECTRA THE 3JHNA COUPLING CONSTANTS FOR DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED FROM A HMQC-J SPECTRUM OF THE 15N-LABELED SAMPLE.

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM SpoIIAA protein, 25 mM NaCl/25 mM K2HPO4/1 mM DTT, pH 7.0, 95% H2O/5% D2Osample_195% H2O/5% D2O
solution20.7 mM [U-15N] SpoIIAA protein, 25 mM NaCl/25 mM K2HPO4/1 mM DTT, pH 7.0, 95% H2O/5% D2Osample_295% H2O/5% D2O
solution30.7 mM [U-13C; U-15N] SpoIIAA protein, 25 mM NaCl/25 mM K2HPO4/1 mM DTT, pH 7.0, 95% H2O/5% D2Osample_395% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSpoIIAA proteinnatural abundance1
0.7 mMSpoIIAA protein[U-15N]2
0.7 mMSpoIIAA protein[U-13C; U-15N]3
25 mMNaClnatural abundance1
25 mMNaClnatural abundance2
25 mMNaClnatural abundance3
25 mMK2HPO4natural abundance1
25 mMK2HPO4natural abundance2
25 mMK2HPO4natural abundance3
1 mMDTTnatural abundance1
1 mMDTTnatural abundance2
1 mMDTTnatural abundance3
Sample conditionsLabel: sample_conditions / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Home-built HOMEBUILTHome-builtHOMEBUILT5001
Home-built HOMEBUILTHome-builtHOMEBUILT7502

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Processing

Software
NameClassification
DYANAmodel building
DYANArefinement
NMR software
NameVersionDeveloperClassification
DYANA1.3GUNTERT,WUTHRICHrefinement
DYANA1.3GUNTERT,WUTHRICHstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT WITH TORSION ANGLE DYNAMICS. THE TOTAL NUMBER OF STEPS WAS 6000; HIGH TEMP. STAGE 1/5TH OF TOTAL. 1000 STEPS OF CONJUGANT GRADIENT MINIMIZATION.
NMR representativeSelection criteria: target function and least restraint violations
NMR ensembleConformer selection criteria: TARGET FUNCTION AND LEAST RESTRAINT VIOLATIONS
Conformers calculated total number: 100 / Conformers submitted total number: 1

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