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- PDB-3gny: Crystal structure of human alpha-defensin 1 (HNP1) -

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Basic information

Entry
Database: PDB / ID: 3gny
TitleCrystal structure of human alpha-defensin 1 (HNP1)
ComponentsNeutrophil defensin 1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / human alpha defensin 1 / human neutrophil peptide 1 / HNP1 / Antibiotic / Antimicrobial / 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 / 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 / estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / azurophil granule lumen / antibacterial humoral response / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPazgier, M. / Lu, W.-Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Through the looking glass, mechanistic insights from enantiomeric human defensins.
Authors: Wei, G. / de Leeuw, E. / Pazgier, M. / Yuan, W. / Zou, G. / Wang, J. / Ericksen, B. / Lu, W.Y. / Lehrer, R.I. / Lu, W.
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 7, 2018Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)7,1245
Polymers6,9042
Non-polymers2203
Water1,08160
1
A: Neutrophil defensin 1
B: Neutrophil defensin 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)14,24810
Polymers13,8084
Non-polymers4396
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3400 Å2
ΔGint-37 kcal/mol
Surface area7580 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-13 kcal/mol
Surface area4180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.466, 31.339, 40.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

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


Mass: 3452.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole, pH 6.5, 1.0 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 14, 2008 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→45.466 Å / Num. all: 8584 / Num. obs: 8119 / % possible obs: 94.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Rsym value: 0.108
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 13.9 / Num. unique all: 719 / Rsym value: 0.152 / % possible all: 85.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0070refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DFN

1dfn


Resolution: 1.56→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.816 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / ESU R: 0.087 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19498 379 4.7 %RANDOM
Rwork0.17133 ---
obs0.17246 7748 94.83 %-
all-8146 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.406 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 0 13 60 549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022504
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.951680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.717558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.37518.18222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8241572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.063158
X-RAY DIFFRACTIONr_chiral_restr0.0910.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021386
X-RAY DIFFRACTIONr_mcbond_it0.6881.5296
X-RAY DIFFRACTIONr_mcangle_it1.1022466
X-RAY DIFFRACTIONr_scbond_it1.7333208
X-RAY DIFFRACTIONr_scangle_it2.6464.5214
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 238 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.595
loose thermal1.9510
LS refinement shellResolution: 1.56→1.604 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 27 -
Rwork0.194 542 -
obs--91.63 %
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)
11.3005-1.0119-0.31254.6970.22262.0005-0.1011-0.0412-0.04160.0810.0667-0.01610.16390.05590.03440.08440.00650.00060.0795-0.00070.07818.08367.40566.0291
23.63052.60390.55673.5465-0.08112.8542-0.0091-0.0177-0.15050.11580.0551-0.208-0.01110.2582-0.0460.06390.0169-0.00450.1058-0.00910.081511.630617.06714.1975
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30

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