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- PDB-4lb7: Crystal structure of human alpha-defensin 1 (HNP1) Y16A/I20A/L25A... -

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Basic information

Entry
Database: PDB / ID: 4lb7
TitleCrystal structure of human alpha-defensin 1 (HNP1) Y16A/I20A/L25A/F28A mutant.
ComponentsNeutrophil defensin 1
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / HUMAN ALPHA DEFENSIN 1 / HUMAN NEUTROPHIL PEPTIDE 1 / HNP1 / ANTIBIOTIC / ANTIVIRAL DEFENSE / DEFENSIN / DISULFIDE BOND / FUNGICIDE / PHOSPHOPROTEIN / SECRETED
Function / homology
Function and homology information


pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / collagen-containing extracellular matrix / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / 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 / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Neutrophil defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsTolbert, W.D. / Wu, X. / Pazgier, M.
CitationJournal: Plos One / Year: 2013
Title: Single, Double and Quadruple Alanine Substitutions at Oligomeric Interfaces Identify Hydrophobicity as the Key Determinant of Human Neutrophil Alpha Defensin HNP1 Function.
Authors: Zhao, L. / Tolbert, W.D. / Ericksen, B. / Zhan, C. / Wu, X. / Yuan, W. / Li, X. / Pazgier, M. / Lu, W.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Neutrophil defensin 1
E: Neutrophil defensin 1
A: Neutrophil defensin 1
B: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)12,7994
Polymers12,7994
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-21 kcal/mol
Surface area6490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.771, 83.771, 51.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide
Neutrophil defensin 1 / Defensin / alpha 1 / HNP-1 / HP-1 / HP1 / HP 1-56 / Neutrophil defensin 2 / HNP-2 / HP-2 / HP2


Mass: 3199.759 Da / Num. of mol.: 4 / Mutation: Y16A, I20A, L25A, F28A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M sodium phosphate monobasic, 0.8 M potassium phosphate monobasic, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 29, 2012 / Details: RH COATED FLAT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 10552 / Num. obs: 10457 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 56
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)/Refmac 5.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GNY

3gny


Resolution: 1.902→24.183 Å / SU ML: 0.28 / σ(F): 1.97 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 1033 9.89 %RANDOM
Rwork0.1998 ---
obs0.2034 10449 99.1 %-
all-10544 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→24.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 0 8 884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007904
X-RAY DIFFRACTIONf_angle_d1.3261204
X-RAY DIFFRACTIONf_dihedral_angle_d11.898312
X-RAY DIFFRACTIONf_chiral_restr0.097120
X-RAY DIFFRACTIONf_plane_restr0.005160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.902-2.00170.35591370.31321350X-RAY DIFFRACTION100
2.0017-2.12710.29611450.29611369X-RAY DIFFRACTION100
2.1271-2.29120.29741550.24241332X-RAY DIFFRACTION100
2.2912-2.52160.27331390.25061387X-RAY DIFFRACTION100
2.5216-2.88590.27411610.22691350X-RAY DIFFRACTION100
2.8859-3.6340.21441670.18871345X-RAY DIFFRACTION100
3.634-24.1830.21461290.17571283X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.05840.35160.32887.1289-2.14595.75-1.3419-0.33940.54420.18110.2948-0.86660.2191-0.77550.94640.7530.0477-0.19010.5144-0.1260.906726.83295.101117.0267
27.1487-0.6928-0.24557.186-2.01857.0078-1.6117-0.64020.53770.05070.8322-0.6604-0.3447-1.22550.87630.75890.2026-0.12420.7944-0.17780.683515.21034.363817.9996
36.3714-0.12010.85516.5762-3.10078.09831.62970.01420.1881-0.6118-0.93070.91140.75980.7448-0.76980.77710.2347-0.0780.5958-0.140.565821.495122.764623.2758
47.6213-0.2789-1.13316.7952-4.52858.96841.6101-0.3669-0.4829-0.4747-0.39631.04510.65260.3065-1.27460.9609-0.0092-0.23850.623-0.10080.831220.319116.084932.6883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 1:30 )D1 - 30
2X-RAY DIFFRACTION2( CHAIN E AND RESID 1:30 )E1 - 30
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1:30 )A1 - 30
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:30 )B1 - 30

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