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- PDB-8qxi: SipA solution structure -

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Basic information

Entry
Database: PDB / ID: 8qxi
TitleSipA solution structure
ComponentsUncharacterized protein SEF0032
KeywordsUNKNOWN FUNCTION / Interacting NblS protein / cyanobacteria
Function / homologyProtein CHLORORESPIRATORY REDUCTION 42-like / Protein CHLORORESPIRATORY REDUCTION 42-like / NADH dehydrogenase complex (plastoquinone) assembly / Uncharacterized protein SEF0032
Function and homology information
Biological speciesSynechocystis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsNeira, J.L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Generalitat ValencianaCIAICO 2021/0135 Spain
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Structure and dynamics of the cyanobacterial regulator SipA.
Authors: Neira, J.L. / Lopez-Redondo, M.L. / Camara-Artigas, A. / Marina, A. / Contreras, A.
History
DepositionOct 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein SEF0032


Theoretical massNumber of molelcules
Total (without water)8,5161
Polymers8,5161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400target function
RepresentativeModel #1target function

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Components

#1: Protein Uncharacterized protein SEF0032


Mass: 8515.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Gene: SEF0032
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8KPR2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
232isotropic13D CBCA(CO)NH
242isotropic13D HNCA
252isotropic13D 1H-15N NOESY
262isotropic13D 1H-15N TOCSY
292isotropic13D HN(CA)CB
282isotropic13D HNCO
272isotropic13D HN(CO)CA
2102isotropic13D H(CCO)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution12.5 mM Regulator protein SipA, 90% H2O/10% D2OpH 5.5, acetic/acetate buffer, 298 K in aqueos solution (natural abundance)natural abundance90% H2O/10% D2O
solution22.5 mM [U-100% 13C; U-100% 15N] Regulator protein SipA, 90% H2O/10% D2OpH 5.5, acetic/acetate buffer, 298 K in aqueos solution (double-labelled sample)15N, 13C sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.5 mMRegulator protein SipAnatural abundance1
2.5 mMRegulator protein SipA[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1pH 5.5, acetic/acetate buffer, 298 K0.050 mMconditions_15.5 1 atm298 K
2pH 5.5, acetic/acetate buffer, 298 K in aqueos solution (double-labelled sample)0.050 mMconditions_25.5 1 atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz / Details: TXI probe

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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