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- PDB-2n4o: Solution structure of the hydrophobin MPG1 from the rice blast fu... -

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Basic information

Entry
Database: PDB / ID: 2n4o
TitleSolution structure of the hydrophobin MPG1 from the rice blast fungus Magnaporthe oryzae
ComponentsHydrophobin-like protein MPG1
KeywordsSTRUCTURAL PROTEIN / amyloid
Function / homologyFungal hydrophobin / Hydrophobin, conserved site / Fungal hydrophobins signature. / Hydrophobin / Hydrophobins / structural constituent of cell wall / fungal-type cell wall / extracellular region / Hydrophobin-like protein MPG1
Function and homology information
Biological speciesMagnaporthe oryzae 70-15 (fungus)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsRey, A.A. / Kwan, A.H. / Sunde, M.
CitationJournal: Sci Rep / Year: 2016
Title: Self-assembly of MPG1, a hydrophobin protein from the rice blast fungus that forms functional amyloid coatings, occurs by a surface-driven mechanism.
Authors: Pham, C.L. / Rey, A. / Lo, V. / Soules, M. / Ren, Q. / Meisl, G. / Knowles, T.P. / Kwan, A.H. / Sunde, M.
History
DepositionJun 25, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrophobin-like protein MPG1


Theoretical massNumber of molelcules
Total (without water)9,8691
Polymers9,8691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hydrophobin-like protein MPG1


Mass: 9869.354 Da / Num. of mol.: 1 / Fragment: residues 19-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae 70-15 (fungus) / Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGCH7_ch7g1089, MGG_10315, MPG1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52751

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1323D HN(CA)CB
1423D HN(CA)CO
1523D CC(CO)NH
1623D H(CCO)NH
1723D CBCA(CO)NH
1823D 1H-15N NOESY
1933D CCH-TOCSY
11023D HNCO
11133D HCAN
11233D HCA(CO)N
11333D 1H-13C NOESY aliphatic
11433D (H)CCH-TOCSY
11512D 1H-15N HSQC
116115N-T2 relaxation measurements

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Sample preparation

Details
Solution-IDContentsSolvent system
1300-400 uM [U-98% 15N] MPG1, 20 mM sodium phosphate, 5 % [U-2H] D2O, 95 % H2O, 0.1 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
2300-400 uM [U-98% 13C; U-98% 15N] MPG1, 20 mM sodium phosphate, 20 uM chloramphenicol, 0.63 mg/mL complete EDTA protease cocktail tablet, 95 % H2O, 5 % [U-99% 2H] D2O, 0.1 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
3300-400 uM [U-98% 13C; U-98% 15N] MPG1, 20 mM sodium phosphate, 20 uM chloramphenicol, 0.63 mg/mL complete EDTA protease cocktail tablet, 100 % [U-99% 2H] D2O, 0.1 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMMPG1-1[U-98% 15N]300-4001
20 mMsodium phosphate-21
5 %D2O-3[U-2H]1
95 %H2O-41
0.1 mMDSS-51
uMMPG1-6[U-98% 13C; U-98% 15N]300-4002
20 mMsodium phosphate-72
20 uMchloramphenicol-82
0.63 mg/mLcomplete EDTA protease cocktail tablet-92
95 %H2O-102
5 %D2O-11[U-99% 2H]2
0.1 mMDSS-122
uMMPG1-13[U-98% 13C; U-98% 15N]300-4003
20 mMsodium phosphate-143
20 uMchloramphenicol-153
0.63 mg/mLcomplete EDTA protease cocktail tablet-163
100 %D2O-17[U-99% 2H]3
0.1 mMDSS-183
Sample conditionsIonic strength: 50 / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.1Goddardchemical shift assignment
Sparky3.1Goddardpeak picking
TALOSTALOS+Cornilescu, Delaglio and Baxdata analysis
TALOSTALOS+Cornilescu, Delaglio and Baxstructure solution
TALOSTALOS+Linge, O'Donoghue and Nilgesdata analysis
TALOSTALOS+Linge, O'Donoghue and Nilgesstructure solution
TALOSTALOS+Cornilescu, Delaglio and Baxdata analysis
TALOSTALOS+Cornilescu, Delaglio and Baxstructure solution
TALOSTALOS+Linge, O'Donoghue and Nilgesdata analysis
TALOSTALOS+Linge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1384 / NOE intraresidue total count: 526 / NOE long range total count: 222 / NOE medium range total count: 154 / NOE sequential total count: 407 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 67 / Protein psi angle constraints total count: 67
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.5 Å

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