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- PDB-9fqb: crystal structure of ClY21-HNP1 -

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Basic information

Entry
Database: PDB / ID: 9fqb
Titlecrystal structure of ClY21-HNP1
ComponentsNeutrophil defensin 1
KeywordsANTIMICROBIAL PROTEIN / 3-chloro-tyrosine modified human alpha-defensin / cationic immune peptide / cystein-rich peptide / tyrosine halogenated HNP1
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 / 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
ACETATE ION / Neutrophil defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsBecker, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: crystal structure of ClY21-HNP1
Authors: Becker, S.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neutrophil defensin 1
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2096
Polymers6,9732
Non-polymers2364
Water1,51384
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-7 kcal/mol
Surface area4290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.075, 46.075, 51.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein/peptide Neutrophil defensin 1 / Defensin / alpha 1 / HNP-1 / HP-1 / HP1


Mass: 3486.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 3-chlorotyrosine at position 21 / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M imidazole, 1.0 M sodium acetate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.09→31.492 Å / Num. obs: 26621 / % possible obs: 99.6 % / Redundancy: 17.6 % / Biso Wilson estimate: 9.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.9
Reflection shellResolution: 1.09→1.109 Å / Num. unique obs: 1252 / CC1/2: 0.909

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.09→31.49 Å / SU ML: 0.0749 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1218 1264 4.76 %
Rwork0.111 25313 -
obs0.1115 26577 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.24 Å2
Refinement stepCycle: LAST / Resolution: 1.09→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms474 0 16 84 574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152537
X-RAY DIFFRACTIONf_angle_d1.5949726
X-RAY DIFFRACTIONf_chiral_restr0.110667
X-RAY DIFFRACTIONf_plane_restr0.021396
X-RAY DIFFRACTIONf_dihedral_angle_d9.454882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.09-1.130.20971250.17412665X-RAY DIFFRACTION96.01
1.13-1.190.16221270.13052796X-RAY DIFFRACTION99.39
1.19-1.250.15411570.11822775X-RAY DIFFRACTION99.76
1.25-1.330.14761590.11482780X-RAY DIFFRACTION99.76
1.33-1.430.1241490.1012779X-RAY DIFFRACTION99.97
1.43-1.570.1071020.09612856X-RAY DIFFRACTION99.97
1.57-1.80.12131770.09982786X-RAY DIFFRACTION99.93
1.8-2.270.09441320.10142884X-RAY DIFFRACTION100
2.27-31.490.121360.11722992X-RAY DIFFRACTION99.68

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