[English] 日本語
Yorodumi- PDB-2l2r: Helical hairpin structure of a novel antimicrobial peptide EcAMP1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l2r | ||||||
---|---|---|---|---|---|---|---|
Title | Helical hairpin structure of a novel antimicrobial peptide EcAMP1 from seeds of barnyard grass (Echinochloa crus-galli) | ||||||
Components | Antimicrobial peptide EcAMP1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / disulfide-stabilized helical hairpin / antifungal peptide / antimicrobial peptide | ||||||
Biological species | Echinochloa crus-galli (barnyard grass) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Nolde, S.B. / Barinov, N.A. / Balashova, T.A. / Arseniev, A.S. / Vassilevski, A.A. / Rogozhin, E.A. / Egorov, T.A. / Grishin, E.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Disulfide-stabilized Helical Hairpin Structure and Activity of a Novel Antifungal Peptide EcAMP1 from Seeds of Barnyard Grass (Echinochloa crus-galli). Authors: Nolde, S.B. / Vassilevski, A.A. / Rogozhin, E.A. / Barinov, N.A. / Balashova, T.A. / Samsonova, O.V. / Baranov, Y.V. / Feofanov, A.V. / Egorov, T.A. / Arseniev, A.S. / Grishin, E.V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2l2r.cif.gz | 221.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2l2r.ent.gz | 187.8 KB | Display | PDB format |
PDBx/mmJSON format | 2l2r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2l2r_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2l2r_full_validation.pdf.gz | 547.4 KB | Display | |
Data in XML | 2l2r_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 2l2r_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/2l2r ftp://data.pdbj.org/pub/pdb/validation_reports/l2/2l2r | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein/peptide | Mass: 4288.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echinochloa crus-galli (barnyard grass) / Organ: SEED |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Micromolar concentrations of EcAMP1 were shown to inhibit growth of several fungal phytopathogens. | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 0.7 mg/mL EcAMP1, 10 mM KOH, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||
Sample conditions | Ionic strength: 10 / pH: 6.62 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing / Software ordinal: 1 Details: Simulated annealing in torsion angle space implemented in CYANA | ||||||||||||
NMR constraints | NOE constraints total: 211 / NOE intraresidue total count: 87 / NOE long range total count: 25 / NOE medium range total count: 33 / NOE sequential total count: 66 / Disulfide bond constraints total count: 6 / Protein chi angle constraints total count: 15 / Protein phi angle constraints total count: 27 | ||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |