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- PDB-4du0: Crystal structure of human alpha-defensin 1, HNP1 (G17A mutant) -

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Basic information

Entry
Database: PDB / ID: 4du0
TitleCrystal structure of human alpha-defensin 1, HNP1 (G17A mutant)
ComponentsNeutrophil defensin 1
KeywordsANTIBIOTIC / cysteine rich antimicrobial peptide / alpha-defensin / HNP1 / human alpha-defensin 1 / G17A mutant / defensin fold / antimicrobial peptide / human neutrophils
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, X. / Lu, W. / Pazgier, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Invariant gly residue is important for alpha-defensin folding, dimerization, and function: a case study of the human neutrophil alpha-defensin HNP1
Authors: Zhao, L. / Ericksen, B. / Wu, X. / Zhan, C. / Yuan, W. / Li, X. / Pazgier, M. / Lu, W.
History
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 13, 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
Revision 1.4Nov 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,30410
Polymers13,8654
Non-polymers4396
Water1,892105
1
A: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6294
Polymers3,4661
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6503
Polymers3,4661
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)3,4661
Polymers3,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5582
Polymers3,4661
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Neutrophil defensin 1
hetero molecules

D: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1876
Polymers6,9322
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area760 Å2
ΔGint-8 kcal/mol
Surface area4310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.453, 50.083, 78.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 3466.137 Da / Num. of mol.: 4 / Fragment: UNP residues 65-94 / Mutation: G81A / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 Magnesium Chloride, 0.1M HEPES, pH7.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2012
RadiationMonochromator: side scattering I-beam bend single crystal, asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 12600 / Num. obs: 12600 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.144 / Rsym value: 0.107 / Net I/σ(I): 18
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.5 / Num. unique all: 625 / Rsym value: 0.981 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1GNY

1gny


Resolution: 1.9→42.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.885 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21219 610 4.9 %RANDOM
Rwork0.17508 ---
all0.17 11994 --
obs0.17683 11946 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.804 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20 Å2
2--0.31 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 26 105 1087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221021
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.9491384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9235120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.89118.18244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59315146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2711516
X-RAY DIFFRACTIONr_chiral_restr0.1460.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021780
X-RAY DIFFRACTIONr_mcbond_it1.0221.5602
X-RAY DIFFRACTIONr_mcangle_it1.6472952
X-RAY DIFFRACTIONr_scbond_it3.0173419
X-RAY DIFFRACTIONr_scangle_it4.6824.5430
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 41 -
Rwork0.221 839 -
obs--95.76 %
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)
10.73550.07780.14463.39111.72081.2955-0.0744-0.08510.1317-0.3113-0.06150.1968-0.2165-0.14070.13590.08270.0137-0.02530.0508-0.04810.07720.43517.622714.8005
21.89260.09930.39225.2620.46622.10050.01580.0778-0.14440.0044-0.156-0.07140.14180.03250.14030.0203-0.00520.00830.0174-0.00280.03342.579910.0530.4713
31.8537-0.6525-0.43193.41564.525712.7749-0.0962-0.22730.19010.01580.3845-0.4892-0.09090.8779-0.28820.012-0.0014-0.00450.1287-0.08640.132814.94522.582916.9444
42.63780.078-0.25930.3002-0.14391.4791-0.01460.1620.2568-0.02480.0420.0679-0.0045-0.0636-0.02740.0056-0.0026-0.00770.04880.03030.042912.870413.318739.5337
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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