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- PDB-2l9y: Solution structure of the MoCVNH-LysM module from the rice blast ... -

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Basic information

Entry
Database: PDB / ID: 2l9y
TitleSolution structure of the MoCVNH-LysM module from the rice blast fungus Magnaporthe oryzae protein (MGG_03307)
ComponentsCVNH-LysM lectin
KeywordsSUGAR BINDING PROTEIN / CVNH / Lectin / Carbohydrate
Function / homology
Function and homology information


Glycine zipper 2TM domain / Glycine zipper 2TM domain / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH ...Glycine zipper 2TM domain / Glycine zipper 2TM domain / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / LysM domain superfamily / Lysin motif / LysM domain / LysM domain profile. / LysM domain / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / LysM domain-containing protein
Similarity search - Component
Biological speciesMagnaporthe oryzae 70-15 (fungus)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKoharudin, L.M.I. / Viscomi, A.R. / Montanini, B. / Kershaw, M.J. / Talbot, N.J. / Ottonello, S. / Gronenborn, A.M.
CitationJournal: Structure / Year: 2011
Title: Structure-Function Analysis of a CVNH-LysM Lectin Expressed during Plant Infection by the Rice Blast Fungus Magnaporthe oryzae.
Authors: Koharudin, L.M. / Viscomi, A.R. / Montanini, B. / Kershaw, M.J. / Talbot, N.J. / Ottonello, S. / Gronenborn, A.M.
History
DepositionFeb 26, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CVNH-LysM lectin


Theoretical massNumber of molelcules
Total (without water)18,1771
Polymers18,1771
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)25 / 1000structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein CVNH-LysM lectin


Mass: 18176.844 Da / Num. of mol.: 1 / Fragment: residues 174-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae 70-15 (fungus) / Description: Expressed as His-tag fusion protein / Gene: MGG_03307 / Plasmid: pET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2 DE3 / References: UniProt: A4R7A7, UniProt: G4N991*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: a type III CVNH
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2223D HN(CA)CB
2323D CBCA(CO)NH
2423D H(CCO)NH
2523D C(CO)NH
2623D (H)CCH-TOCSY
2723D 1H-15N NOESY
2823D 1H-13C NOESY aliphatic
1912D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-100% 15N]1
0.5 mMprotein-2[U-100% 13C; U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.025ambient 298 K
20.025ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.2.2_01Johnson, One Moon Scientificdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichautomatic noe assignment
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the 25 lowest energy structures were further refined using explicit water.
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 81 / Protein psi angle constraints total count: 80
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.042 Å / Distance rms dev error: 0.001 Å

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