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- PDB-1p9z: The Solution Structure of Antifungal Peptide Distinct With a Five... -

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Basic information

Entry
Database: PDB / ID: 1p9z
TitleThe Solution Structure of Antifungal Peptide Distinct With a Five-disulfide Motif from Eucommia ulmoides Oliver
ComponentsEucommia Antifungal peptide 2
KeywordsANTIFUNGAL PROTEIN / Antifungal peptide / Chitin-binding peptide / Disulfide stabilized motif
Function / homology
Function and homology information


chitin binding / defense response to fungus / killing of cells of another organism
Similarity search - Function
Endochitinase-like / Chitin-binding, type 1, conserved site / Chitin recognition or binding domain signature. / Chitin-binding type-1 domain profile. / Chitin binding domain / Chitin-binding, type 1 / Endochitinase-like superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antifungal peptide 2
Similarity search - Component
Biological speciesEucommia ulmoides (plant)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsHuang, R.H. / Xiang, Y. / Tu, G.Z. / Zhang, Y. / Wang, D.C.
Citation
Journal: Biochemistry / Year: 2004
Title: Solution Structure of Eucommia Antifungal Peptide: A Novel Structural Model Distinct with a Five-Disulfide Motif.
Authors: Huang, R.H. / Xiang, Y. / Tu, G.Z. / Zhang, Y. / Wang, D.C.
#1: Journal: FEBS Lett. / Year: 2002
Title: Two novel antifungal peptides distinct with a five-disulfide motif fron the bark of Eucommia ulmoides Oliver
Authors: Huang, R.H. / Xiang, Y. / Liu, X.Z. / Zhang, Y. / Hu, Z. / Wang, D.C.
History
DepositionMay 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_nmr_software ...entity_poly / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 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
Remark 650Helix determination method: Author determined
Remark 700Sheet determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eucommia Antifungal peptide 2


Theoretical massNumber of molelcules
Total (without water)4,1731
Polymers4,1731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

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Components

#1: Protein/peptide Eucommia Antifungal peptide 2


Mass: 4172.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: EAFP2 / Source: (natural) Eucommia ulmoides (plant) / Tissue: Bark / References: UniProt: P83597
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D TOCSY
1312D NOESY
2422D TOCSY
2522D NOESY
262DQF-COSY
3712D NOESY
3812D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
16mM antifungal peptide(EAFP2); 20 mM phosphate buffer,0.01 mM EDTA90% H2O/10% D2O
26mM antifungal peptide(EAFP2); 20 mM phosphate buffer, 0.01 mMEDTA100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM Phospate Buffer 5.6ambient 300 K
220 mM Phospate Buffer 5.6ambient 300 K
320 mM Phospate Buffer 5.6ambient 290 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Bruker Corp.collection
Sparky3.105Goddard, T.D. and Kneller, D.G.data analysis
CNS1.1Brunger, A.T. etc.structure solution
CNS1.1Brunger, A.T. etc.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 630 restraints, 594 are NOE-derived distance constraints, 16 dihedral angle restraints,20 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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