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- PDB-1fry: THE SOLUTION STRUCTURE OF SHEEP MYELOID ANTIMICROBIAL PEPTIDE, RE... -

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Entry
Database: PDB / ID: 1fry
TitleTHE SOLUTION STRUCTURE OF SHEEP MYELOID ANTIMICROBIAL PEPTIDE, RESIDUES 1-29 (SMAP29)
ComponentsMYELOID ANTIMICROBIAL PEPTIDE
KeywordsANTIMICROBIAL PROTEIN / random-ordered coil-loop
Function / homology
Function and homology information


antibacterial innate immune response / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular space
Similarity search - Function
Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
Cathelin-related peptide SC5
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTack, B.F. / Sawai, M.V. / Kearney, W.R. / Robertson, A.D. / Sherman, M.A. / Wang, W. / Hong, T. / Boo, L.M. / Wu, H. / Waring, A.J. / Lehrer, R.I.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: SMAP-29 has two LPS-binding sites and a central hinge.
Authors: Tack, B.F. / Sawai, M.V. / Kearney, W.R. / Robertson, A.D. / Sherman, M.A. / Wang, W. / Hong, T. / Boo, L.M. / Wu, H. / Waring, A.J. / Lehrer, R.I.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: MYELOID ANTIMICROBIAL PEPTIDE


Theoretical massNumber of molelcules
Total (without water)3,2661
Polymers3,2661
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)40 / 300structures with acceptable covalent geometry, structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1,21lowest energy

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Components

#1: Protein/peptide MYELOID ANTIMICROBIAL PEPTIDE / SMAP29 / SMAP-29 GENE PRODUCT


Mass: 3266.037 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in sheep. NMR samples were synthesized using FMOC chemistry
References: UniProt: P49928

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1mM smap29; 50mM phosphate buffer, pH 5.94 / Solvent system: 60% H2O, 40% D3-trifluoroethanol
Sample conditionsIonic strength: ca. 50mM / pH: 5.94 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionClassification
DYANA1.5structure solution
VNMR4.3bcollection
VNMR6.1bdata analysis
VNMR6.1brefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Structure based on 217 noe contstraints and 8 HA-NH coupling constants
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 40

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