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- PDB-5noc: Solution NMR Structure of the C-terminal domain of ParB (Spo0J) -

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Basic information

Entry
Database: PDB / ID: 5noc
TitleSolution NMR Structure of the C-terminal domain of ParB (Spo0J)
ComponentsStage 0 sporulation protein J
KeywordsDNA BINDING PROTEIN / homodimer / bacterial / chromosome / segregation / centromere
Function / homology
Function and homology information


positive regulation of sporulation resulting in formation of a cellular spore / bacterial nucleoid / sporulation resulting in formation of a cellular spore / chromosome segregation / chromosome / DNA binding
Similarity search - Function
ParB/Spo0J, HTH domain / HTH domain found in ParB protein / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily
Similarity search - Domain/homology
Stage 0 sporulation protein J
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHigman, V.A. / Fisher, G.L.M. / Dillingham, M.S. / Crump, M.P.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust100401/Z/12/Z United Kingdom
Biotechnology and Biological Sciences Research Council1363883 United Kingdom
CitationJournal: Elife / Year: 2017
Title: The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere.
Authors: Fisher, G.L. / Pastrana, C.L. / Higman, V.A. / Koh, A. / Taylor, J.A. / Butterer, A. / Craggs, T. / Sobott, F. / Murray, H. / Crump, M.P. / Moreno-Herrero, F. / Dillingham, M.S.
History
DepositionApr 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 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: Stage 0 sporulation protein J
B: Stage 0 sporulation protein J


Theoretical massNumber of molelcules
Total (without water)16,2222
Polymers16,2222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3190 Å2
ΔGint-15 kcal/mol
Surface area6150 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Stage 0 sporulation protein J


Mass: 8111.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: spo0J, BSU40960 / Production host: Escherichia coli (E. coli) / References: UniProt: P26497

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic13D HNCO
142isotropic13D HNCA
152isotropic13D HN(CO)CA
162isotropic13D HN(CA)CB
172isotropic13D CBCA(CO)NH
182isotropic13D C(CO)NH
192isotropic13D H(CCO)NH
1102isotropic13D (H)CCH-TOCSY
1112isotropic13D 1H-15N NOESY
1122isotropic13D 1H-13C NOESY aliphatic
1132isotropic13D 1H-13C NOESY aromatic
1141isotropic12D 1H-1H TOCSY
1151isotropic12D 1H-1H NOESY
1163isotropic13D 13C,15N F1-filtered, 13C,15N F3-edited 13C-NOSEY-HSQC
1173isotropic13D 13C,15N F1-filtered, 13C,15N F3-edited 15N-NOSEY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution13 mM ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2Ounlabelled95% H2O/5% D2O
solution23 mM [U-13C; U-15N] ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2O15N13C95% H2O/5% D2O
solution31.5 mM ParB (Spo0J), 1.5 mM [U-13C; U-15N] ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2Omixed_labelled95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMParB (Spo0J)natural abundance1
137 mMsodium chloridenatural abundance1
2.7 mMpotassium chloridenatural abundance1
10 mMNa2HPO4natural abundance1
1.8 mMKH2PO4natural abundance1
3 mMParB (Spo0J)[U-13C; U-15N]2
137 mMsodium chloridenatural abundance2
2.7 mMpotassium chloridenatural abundance2
10 mMNa2HPO4natural abundance2
1.8 mMKH2PO4natural abundance2
1.5 mMParB (Spo0J)natural abundance3
1.5 mMParB (Spo0J)-label[U-13C; U-15N]3
137 mMsodium chloridenatural abundance3
2.7 mMpotassium chloridenatural abundance3
10 mMNa2HPO4natural abundance3
1.8 mMKH2PO4natural abundance3
Sample conditionsIonic strength: 150 mM / Label: standard / pH: 6.1 / Pressure: 1 atm / Temperature: 208 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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