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- PDB-2n1s: Spatial Structure of Antimicrobial Peptide SmAMP2-2c from Seeds o... -

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Basic information

Entry
Database: PDB / ID: 2n1s
TitleSpatial Structure of Antimicrobial Peptide SmAMP2-2c from Seeds of Stellaria media
ComponentsAMP-2
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial Peptide / ICK / cystine knot inhibitor / cystine knot
Function / homologyChitin-binding, type 1, conserved site / Chitin recognition protein / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / chitin binding / Antimicrobial peptide 2
Function and homology information
Biological speciesStellaria media (plant)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsBozin, T.N. / Bocharov, E.V.
CitationJournal: To be Published
Title: Common chickweed (Stellaria media) antifungal peptides with chitin-binding domain provide unique plant defense strategy.
Authors: Vassilevski, A.A. / Bozin, T.N. / Musolyamov, A.K. / Panova, S.V. / Slavokhotova, A.A. / Mitkevich, V.A. / Finkina, E.I. / Nikonorova, A.K. / Ovchinnikova, T.V. / Arseniev, A.S. / Babakov, A. ...Authors: Vassilevski, A.A. / Bozin, T.N. / Musolyamov, A.K. / Panova, S.V. / Slavokhotova, A.A. / Mitkevich, V.A. / Finkina, E.I. / Nikonorova, A.K. / Ovchinnikova, T.V. / Arseniev, A.S. / Babakov, A.V. / Bocharov, E.V. / Grishin, E.V. / Egorov, T.A.
History
DepositionApr 16, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: AMP-2


Theoretical massNumber of molelcules
Total (without water)3,0021
Polymers3,0021
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide AMP-2


Mass: 3002.417 Da / Num. of mol.: 1 / Fragment: residues 68-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stellaria media (plant) / Gene: amp-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: E1UYU0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D DQF-COSY
1222D 1H-13C HSQC
1332D 1H-1H NOESY
3432D 1H-1H TOCSY
1512D 1H-1H TOCSY
2612D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM SmAMP2-2c, 20 mM sodium acetate, 30 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM SmAMP2-2c, 20 mM sodium acetate, 30 mM sodium chloride, 100% D2O100% D2O
32 mM SmAMP2-2c, 10 mM sodium acetate, 70 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.8 mMSmAMP2-2c-11
20 mMsodium acetate-21
30 mMsodium chloride-31
0.8 mMSmAMP2-2c-42
20 mMsodium acetate-52
30 mMsodium chloride-62
2 mMSmAMP2-2c-73
10 mMsodium acetate-83
70 mMsodium chloride-93
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.08 4.5 ambient 303 K
20.05 4.5 ambient 283 K
30.05 4.5 ambient 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7002
Bruker DRXBrukerDRX8003

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Processing

NMR software
NameVersionDeveloperClassification
MolmolKoradi, Billeter and Wuthrichmolecule viewer
CYANA2.1Guntert, Braun and Wuthrichstructure solution
ACMEDelaglio, Zhengrong and Baxj-coupling measurement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CARAKeller and Wuthrichchemical shift assignment
CYANAKeller and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 237 / NOE intraresidue total count: 60 / NOE long range total count: 64 / NOE medium range total count: 43 / NOE sequential total count: 70 / Disulfide bond constraints total count: 18 / Hydrogen bond constraints total count: 64 / Protein chi angle constraints total count: 16 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.03 Å / Maximum torsion angle constraint violation: 3.08 ° / Maximum upper distance constraint violation: 0.39 Å

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