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- PDB-4lbf: Crystal structure of HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A mutant -

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Basic information

Entry
Database: PDB / ID: 4lbf
TitleCrystal structure of HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A mutant
ComponentsNeutrophil defensin 1
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / HUMAN ALPHA DEFENSIN 1 / HUMAN NEUTROPHIL PEPTIDE 1 / ANTIBIOTIC / ANTIVIRAL DEFENSE / DEFENSIN / DISULFIDE BOND / FUNGICIDE / PHOSPHOPROTEIN / SECRETED
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
Neutrophil defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 ...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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Neutrophil defensin 1
D: Neutrophil defensin 1
E: Neutrophil defensin 1
F: Neutrophil defensin 1
G: Neutrophil defensin 1
H: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0369
Polymers26,9448
Non-polymers921
Water3,765209
1
A: Neutrophil defensin 1
B: Neutrophil defensin 1
C: Neutrophil defensin 1
D: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5645
Polymers13,4724
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-21 kcal/mol
Surface area6910 Å2
MethodPISA
2
E: Neutrophil defensin 1
F: Neutrophil defensin 1
G: Neutrophil defensin 1
H: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)13,4724
Polymers13,4724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-21 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.002, 62.575, 42.498
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number5
Space group name H-MC121

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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: 3367.951 Da / Num. of mol.: 8 / Mutation: I20A, L25A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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: 1.82 Å3/Da / Density % sol: 32.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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: May 27, 2009 / Details: CONFOCAL
RadiationMonochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 22854 / Num. obs: 22465 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.5
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.6 / % possible all: 84.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GNY

3gny


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.857 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23088 1085 5.1 %RANDOM
Rwork0.1851 ---
obs0.18765 20118 99.18 %-
all-20466 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å21.93 Å2
2---0.36 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 6 209 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221895
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9222567
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7775226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.46118.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.615250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081531
X-RAY DIFFRACTIONr_chiral_restr0.1550.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211503
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1611.51159
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72721801
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9043736
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3794.5766
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 83 -
Rwork0.272 1441 -
obs--96.76 %

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