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- PDB-5u87: NMR structure of the precursor protein PawS1 comprising SFTI-1 an... -

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Basic information

Entry
Database: PDB / ID: 5u87
TitleNMR structure of the precursor protein PawS1 comprising SFTI-1 and a seed storage albumin
ComponentsPreproalbumin PawS1
KeywordsPLANT PROTEIN / trypsin inhibitor / SFTI-1 / seed storage albumin / Structure from MOLMOL
Function / homologyNapin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / Preproalbumin PawS1
Function and homology information
Biological speciesHelianthus annuus (common sunflower)
MethodSOLUTION NMR / simulated annealing
AuthorsFranke, B. / James, A.M. / Mobli, M. / Colgrave, M.L. / Mylne, J.S. / Rosengren, K.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120103369 Australia
CitationJournal: to be published
Title: NMR structure of the precursor protein PawS1 comprising SFTI-1 and a seed storage albumin
Authors: Franke, B. / James, A.M. / Mobli, M. / Colgrave, M.L. / Mylne, J.S. / Rosengren, K.J.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support / Item: _entity.pdbx_number_of_molecules
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
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 / _struct_conn.pdbx_dist_value
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Preproalbumin PawS1


Theoretical massNumber of molelcules
Total (without water)13,2801
Polymers13,2801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1molprobity

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Components

#1: Protein Preproalbumin PawS1


Mass: 13280.334 Da / Num. of mol.: 1 / Fragment: UNP residues 36-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helianthus annuus (common sunflower) / Gene: PawS1 / Production host: Escherichia coli (E. coli) / References: UniProt: H2L0T2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HBHA(CO)NH
171isotropic13D H(CC)(CO)NH-TOCSY
181isotropic13D (H)CC(CO)NH-TOCSY
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 3.9 mg/mL [U-13C; U-15N] Proalbumin PawS1, 90% H2O/10% D2O
Label: Proalbumin PawS1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 3.9 mg/mL / Component: Proalbumin PawS1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0 mM / Label: Proalbumin PawS1 / pH: 4.62 / Pressure: ambient bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: equipped with cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNMRCCPNpeak picking
TopSpin2.1Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 2
Details: Final structures were calculated and waterminimised using cartesian dynamics in CNS.
NMR representativeSelection criteria: molprobity
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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