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- PDB-6h0i: Solution structure of Melampsora larici-populina MlpP4.1 -

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Basic information

Entry
Database: PDB / ID: 6h0i
TitleSolution structure of Melampsora larici-populina MlpP4.1
ComponentsSecreted protein
KeywordsUNKNOWN FUNCTION / cysteine knot protein / poplar rust / effector
Function / homologySecreted protein
Function and homology information
Biological speciesMelampsora larici-populina 98AG31 (fungus)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTsan, P. / Petre, B. / Hecker, A. / Rouhier, N. / Duplessis, S.
CitationJournal: Sci Rep / Year: 2019
Title: Structural genomics applied to the rust fungus Melampsora larici-populina reveals two candidate effector proteins adopting cystine knot and NTF2-like protein folds.
Authors: de Guillen, K. / Lorrain, C. / Tsan, P. / Barthe, P. / Petre, B. / Saveleva, N. / Rouhier, N. / Duplessis, S. / Padilla, A. / Hecker, A.
History
DepositionJul 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Dec 18, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Secreted protein


Theoretical massNumber of molelcules
Total (without water)7,9791
Polymers7,9791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5750 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #14closest to the average

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Components

#1: Protein Secreted protein


Mass: 7978.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melampsora larici-populina 98AG31 (fungus)
Gene: MELLADRAFT_124266 / Production host: Escherichia coli (E. coli) / References: UniProt: F4RME6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-15N TOCSY
131isotropic13D HNCA
141isotropic13D HNHA
151isotropic13D HNHB

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Sample preparation

DetailsType: solution
Contents: 50 mM potassium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O
Label: 15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMpotassium phosphatenatural abundance1
0.02 %sodium azidenatural abundance1
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
TopSpinBruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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