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Yorodumi- PDB-2l9y: Solution structure of the MoCVNH-LysM module from the rice blast ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l9y | ||||||
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Title | Solution structure of the MoCVNH-LysM module from the rice blast fungus Magnaporthe oryzae protein (MGG_03307) | ||||||
Components | CVNH-LysM lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / CVNH / Lectin / Carbohydrate | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Magnaporthe oryzae 70-15 (fungus) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Koharudin, L.M.I. / Viscomi, A.R. / Montanini, B. / Kershaw, M.J. / Talbot, N.J. / Ottonello, S. / Gronenborn, A.M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l9y.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2l9y.ent.gz | 1007.6 KB | Display | PDB format |
PDBx/mmJSON format | 2l9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/2l9y ftp://data.pdbj.org/pub/pdb/validation_reports/l9/2l9y | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: SOLUTION NMR / Details: a type III CVNH | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: the 25 lowest energy structures were further refined using explicit water. | ||||||||||||||||||||||||||||
NMR constraints | Protein 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 representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Average 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 rms | Distance rms dev: 0.042 Å / Distance rms dev error: 0.001 Å |