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- PDB-1dfn: CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHAN... -

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Basic information

Entry
Database: PDB / ID: 1dfn
TitleCRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION
ComponentsDEFENSIN HNP-3
KeywordsDEFENSIN
Function / homology
Function and homology information


pore-forming activity / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa ...pore-forming activity / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / azurophil granule lumen / antibacterial humoral response / : / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to virus / killing of cells of another organism / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Neutrophil defensin 1 / Neutrophil defensin 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHill, C.P. / Yee, J. / Selsted, M.E. / Eisenberg, D.
Citation
Journal: Science / Year: 1991
Title: Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization.
Authors: Hill, C.P. / Yee, J. / Selsted, M.E. / Eisenberg, D.
#1: Journal: J.Clin.Invest. / Year: 1985
Title: Primary Structures of Three Human Neutrophil Defensins
Authors: Selsted, M.E. / Harwig, S.S.L. / Ganz, T. / Schilling, J.W. / Lehrer, R.I.
#2: Journal: J.Clin.Invest. / Year: 1985
Title: Defensins. Natural Peptide Antibiotics of Human Neutrophils
Authors: Ganz, T. / Selsted, M.E. / Szklarek, D. / Harwig, S.S.L. / Daher, K. / Bainton, D.F. / Lehrer, R.I.
History
DepositionJan 18, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Category: pdbx_database_status / struct_conf / Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 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 / _pdbx_entry_details.has_protein_modification
Remark 700SHEET THERE IS A CLASSIC BULGE INVOLVING RESIDUES 17, 18, AND 29 FOR EACH OF THE CHAINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEFENSIN HNP-3
B: DEFENSIN HNP-3


Theoretical massNumber of molelcules
Total (without water)6,9922
Polymers6,9922
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-9 kcal/mol
Surface area4160 Å2
MethodPISA
2
A: DEFENSIN HNP-3
B: DEFENSIN HNP-3

A: DEFENSIN HNP-3
B: DEFENSIN HNP-3


Theoretical massNumber of molelcules
Total (without water)13,9844
Polymers13,9844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2400 Å2
ΔGint-28 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.800, 45.000, 40.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: RESIDUES A 8 AND B 8 ARE CIS PROLINES.
2: THERE IS A CLASSIC BULGE INVOLVING RESIDUES 17, 18, AND 29 FOR EACH OF THE CHAINS.
Components on special symmetry positions
IDModelComponents
11B-35-

HOH

DetailsTHE TWO MOLECULES IN THE ASYMMETRIC UNIT HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. EACH OF THE TWO MONOMERS IN THE ASYMMETRIC UNIT CONTAINS A THREE STRAND ANTIPARALLEL SHEET. A LOCAL TWO-FOLD AXIS RELATING MOLECULES *A* AND *B* RESULTS IN A SIX-STRANDED ANTIPARALLEL SHEET IN THE DIMER. THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED TO EACH OTHER BY A LOCAL TWO-FOLD AXIS.

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Components

#1: Protein/peptide DEFENSIN HNP-3


Mass: 3496.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P59665, UniProt: P59666*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 30 RESIDUES IN HNP-3 HAVE BEEN NUMBERED FROM 2 - 31 IN ORDER TO BETTER FIT THE SEQUENCE ...THE 30 RESIDUES IN HNP-3 HAVE BEEN NUMBERED FROM 2 - 31 IN ORDER TO BETTER FIT THE SEQUENCE ALIGNMENT WITH OTHER DEFENSIN MOLECULES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.39 %
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.01 %acetic acid1drop
315 %PEG80001reservoir
410 %isopropanol1reservoir
5100 mMsodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 4524 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Num. measured all: 22975 / Rmerge F obs: 0.054 / Biso Wilson estimate: 15.6 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→10 Å / Rfactor obs: 0.19
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 0 44 514
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9911
X-RAY DIFFRACTIONp_mcangle_it1.721.5
X-RAY DIFFRACTIONp_scbond_it1.5651
X-RAY DIFFRACTIONp_scangle_it2.4271.5
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.180.15
X-RAY DIFFRACTIONp_singtor_nbd0.2040.5
X-RAY DIFFRACTIONp_multtor_nbd0.2740.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1810.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.83
X-RAY DIFFRACTIONp_staggered_tor18.215
X-RAY DIFFRACTIONp_orthonormal_tor28.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. reflection all: 4448 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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