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- PDB-6g7g: Structure of SPH (Self-Incompatibility Protein Homologue) protein... -

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Basic information

Entry
Database: PDB / ID: 6g7g
TitleStructure of SPH (Self-Incompatibility Protein Homologue) proteins, a widespread family of small, highly stable, secreted proteins from plants
ComponentsS-protein homolog 15
KeywordsPLANT PROTEIN / Self-Incompatibility Protein Homolog / Origami strain E coli
Function / homologyPlant self-incompatibility S1 / Plant self-incompatibility protein S1 / rejection of self pollen / extracellular region / S-protein homolog 15
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRajasekar, K.V. / Coulthard, R.J. / Ride, J.P. / Ji, S. / Winn, P.J. / Wheeler, M.P. / Hyde, E.I. / Smith, L.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust099185/Z/12/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2019
Title: Structure of SPH (self-incompatibility protein homologue) proteins: a widespread family of small, highly stable, secreted proteins.
Authors: Rajasekar, K.V. / Ji, S. / Coulthard, R.J. / Ride, J.P. / Reynolds, G.L. / Winn, P.J. / Wheeler, M.J. / Hyde, E.I. / Smith, L.J.
History
DepositionApr 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-protein homolog 15


Theoretical massNumber of molelcules
Total (without water)13,5861
Polymers13,5861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, AUC
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6910 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 S-protein homolog 15


Mass: 13585.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SPH15, At5g39493, MUL8.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FLY6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HN(COCA)CB
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CO
1111isotropic13D HBHA(CO)NH
1101isotropic13D (H)CCH-COSY
192isotropic13D (H)CCH-TOCSY
182isotropic23D 1H-15N TOCSY
172isotropic23D 1H-15N NOESY
162isotropic33D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.3 mM [U-13C; U-15N] Sph15, 95% H2O/5% D2OSample_195% H2O/5% D2O
solution21 mM [U-13C; U-15N] Sph15, 95% H2O/5% D2OSample_295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMSph15[U-13C; U-15N]1
1 mMSph15[U-13C; U-15N]2
Sample conditionsIonic strength: 0.01 M / Ionic strength err: 0.005 / Label: Sph15 / pH: 5.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA8002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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