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- PDB-4lbb: Crystal structure of human alpha-defensin 1 (HNP1) I20A mutant -

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Basic information

Entry
Database: PDB / ID: 4lbb
TitleCrystal structure of human alpha-defensin 1 (HNP1) I20A 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.719 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,0338
Polymers6,8202
Non-polymers2136
Water46826
1
A: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4452
Polymers3,4101
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5876
Polymers3,4101
Non-polymers1775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.745, 37.745, 40.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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: 3410.031 Da / Num. of mol.: 2 / Mutation: I20A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 0.1 M Tris-HCl pH 8.5, 0.2 M lithium sulfate, 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 18, 2009 / Details: CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 8953 / Num. obs: 8953 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 12.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2 / % possible all: 99

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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: 1.719→27.615 Å / SU ML: 0.12 / σ(F): 1.38 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 276 4.6 %RANDOM
Rwork0.2012 ---
obs0.2023 5994 97.89 %-
all-5994 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.719→27.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 6 26 502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015488
X-RAY DIFFRACTIONf_angle_d1.642650
X-RAY DIFFRACTIONf_dihedral_angle_d12.361170
X-RAY DIFFRACTIONf_chiral_restr0.1262
X-RAY DIFFRACTIONf_plane_restr0.00884
LS refinement shellResolution: 1.719→2.1658 Å
RfactorNum. reflection% reflection
Rfree0.2585 132 -
Rwork0.2318 2775 -
obs--96 %
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)
14.7525-1.3322-0.0198.52051.96445.5223-0.18910.21460.4072-0.14180.16190.23640.1875-0.24120.16410.2749-0.0074-0.0150.25280.01560.26855.982-1.4018-1.324
24.29381.2387-1.5568.8269-2.32455.9053-0.0864-0.20650.27320.14280.0946-0.23560.22480.27750.08950.19160.0057-0.02040.2247-0.02130.206712.909617.4254-4.8854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:30 )A1 - 30
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:30 )B1 - 30

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