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- PDB-1fqq: SOLUTION STRUCTURE OF HUMAN BETA-DEFENSIN-2 -

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Basic information

Entry
Database: PDB / ID: 1fqq
TitleSOLUTION STRUCTURE OF HUMAN BETA-DEFENSIN-2
ComponentsBETA-DEFENSIN-2Beta defensin
KeywordsANTIBIOTIC / DEFENSIN / SOLUTION STRUCTURE
Function / homology
Function and homology information


CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis ...CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Antimicrobial Peptide, Beta-defensin 2; Chain A / Antimicrobial Peptide, Beta-defensin 2; Chain A / Beta defensin type / Beta defensin / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Simulated annealing, torsion angle dynamics
AuthorsSawai, M.V. / Jia, H.P. / Liu, L. / Aseyev, V. / Wiencek, J.M. / McCray Jr., P.B. / Ganz, T. / Kearney, W.R. / Tack, B.F.
CitationJournal: Biochemistry / Year: 2001
Title: The NMR structure of human beta-defensin-2 reveals a novel alpha-helical segment.
Authors: Sawai, M.V. / Jia, H.P. / Liu, L. / Aseyev, V. / Wiencek, J.M. / McCray Jr., P.B. / Ganz, T. / Kearney, W.R. / Tack, B.F.
History
DepositionSep 6, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 24, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-DEFENSIN-2


Theoretical massNumber of molelcules
Total (without water)4,3421
Polymers4,3421
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2970 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest target function value
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide BETA-DEFENSIN-2 / Beta defensin


Mass: 4342.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O15263

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY,DOF-COSY,TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 0.9mM Human Beta-Defensin-2; 45mM sodium phosphate buffer
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.045 / pH: 3.7 / Pressure: 1013 hpa / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: Simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest target function value
Conformers calculated total number: 100 / Conformers submitted total number: 20

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