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- PDB-2lw6: Solution structure of an avirulence protein AvrPiz-t from pathoge... -

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Basic information

Entry
Database: PDB / ID: 2lw6
TitleSolution structure of an avirulence protein AvrPiz-t from pathogen Magnaportheoryzae
ComponentsAvrPiz-t protein
KeywordsAPOPTOSIS / AvrPiz-t / plant resistance gene / avirulence protein / protein degradation
Function / homologymini-chromosome maintenance (MCM) complex, domain 2 - #40 / Avirulence protein AvrPiz-t / mini-chromosome maintenance (MCM) complex, domain 2 / Sandwich / Mainly Beta / AvrPiz-t
Function and homology information
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics
Model detailslowest energy, model20
AuthorsZhang, Z.-M. / Zhang, X. / Zhou, Z. / Hu, H. / Liu, M. / Zhou, B. / Zhou, J.
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: Solution structure of the Magnaporthe oryzae avirulence protein AvrPiz-t.
Authors: Zhang, Z.-M. / Zhang, X. / Zhou, Z.R. / Hu, H.Y. / Liu, M. / Zhou, B. / Zhou, J.
History
DepositionJul 23, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Oct 16, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AvrPiz-t protein


Theoretical massNumber of molelcules
Total (without water)8,7511
Polymers8,7511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein AvrPiz-t protein


Mass: 8750.991 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: 7bg7.13 / Production host: Escherichia coli (E. coli) / References: UniProt: H2DQR0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CO)CA
1713D (H)CCH-TOCSY
1813D 1H-15N TOCSY
2922D 1H-15N HSQC
11013D 1H-13C NOESY
11113D HN(CA)CB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 13C; U-100% 15N] H2O-1, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-99% 15N] D2O-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMH2O-1[U-100% 13C; U-100% 15N]1
0.3 mMD2O-2[U-99% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1506.5ambient 293 K
26.5293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker INOVABrukerINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIALinge, O'Donoghue and Nilgesprocessing
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: distance geometry, 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 / Representative conformer: 20

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