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- PDB-3lvx: Crystal structure of human alpha-defensin 1 (I6A mutant) -

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Basic information

Entry
Database: PDB / ID: 3lvx
TitleCrystal structure of human alpha-defensin 1 (I6A mutant)
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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPazgier, M. / Lu, W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Trp-26 imparts functional versatility to human alpha-defensin HNP1.
Authors: Wei, G. / Pazgier, M. / de Leeuw, E. / Rajabi, M. / Li, J. / Zou, G. / Jung, G. / Yuan, W. / Lu, W.Y. / Lehrer, R.I. / Lu, W.
History
DepositionFeb 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)7,1045
Polymers6,8202
Non-polymers2843
Water1,78399
1
A: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5983
Polymers3,4101
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5062
Polymers3,4101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Neutrophil defensin 1
B: Neutrophil defensin 1
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)170,503120
Polymers163,68148
Non-polymers6,82172
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation33_545y,z-1/2,x+1/21
crystal symmetry operation34_545-y,z-1/2,-x+1/21
crystal symmetry operation35_555y,-z+1/2,-x+1/21
crystal symmetry operation36_555-y,-z+1/2,x+1/21
crystal symmetry operation41_545x,z-1/2,-y+1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_555-x,-z+1/2,-y+1/21
crystal symmetry operation44_555x,-z+1/2,y+1/21
crystal symmetry operation53_455z-1/2,x,y+1/21
crystal symmetry operation54_455z-1/2,-x,-y+1/21
crystal symmetry operation55_555-z+1/2,-x,y+1/21
crystal symmetry operation56_555-z+1/2,x,-y+1/21
crystal symmetry operation69_455z-1/2,y,-x+1/21
crystal symmetry operation70_455z-1/2,-y,x+1/21
crystal symmetry operation71_555-z+1/2,y,x+1/21
crystal symmetry operation72_555-z+1/2,-y,-x+1/21
Buried area65290 Å2
ΔGint-1188 kcal/mol
Surface area69820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.069, 118.069, 118.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-45-

HOH

21A-64-

HOH

31A-79-

HOH

41A-85-

HOH

51A-87-

HOH

61A-92-

HOH

Detailsbiological unit is half of asymmetric unit.

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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: 3410.031 Da / Num. of mol.: 2 / Fragment: HUMAN NEUTROPHIL DEFENSIN 1 / Mutation: I6A / Source method: obtained synthetically / Details: Protein is naturally found in Homo sapiens (human) / References: UniProt: P59665
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG 400; 0.1 M HEPES-Na, pH 7.5; 2 M ammonium sulfate, 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: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→68.167 Å / Num. all: 9313 / Num. obs: 9272 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Rmerge(I) obs: 0.161 / Rsym value: 0.114 / Net I/σ(I): 17.4
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / Rsym value: 0.729 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GNY

3gny


Resolution: 1.63→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 3.026 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.174 442 4.8 %RANDOM
Rwork0.1684 ---
obs0.16868 8811 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.48 Å2
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 16 99 585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.958679
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.529558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.5718.18222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2531568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.362158
X-RAY DIFFRACTIONr_chiral_restr0.0940.262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021386
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_it0.6411.5296
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.122462
X-RAY DIFFRACTIONr_scbond_it2.3083205
X-RAY DIFFRACTIONr_scangle_it3.7874.5217
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.631→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 23 -
Rwork0.269 604 -
obs--95.73 %
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)
11.26610.47260.13731.4745-0.07821.76250.02650.0313-0.0619-0.0442-0.02740.02030.0396-0.04250.00080.00670.00420.00010.0079-0.00450.0135-18.151814.535527.23
22.27010.2266-0.1341.76520.24390.6547-0.01360.134-0.13950.01860.0495-0.10240.11760.1304-0.03590.03210.0127-0.00230.0543-0.01430.0292-7.107212.48633.9063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION1A31 - 3968
3X-RAY DIFFRACTION1A32 - 101
4X-RAY DIFFRACTION2B1 - 30
5X-RAY DIFFRACTION2B31
6X-RAY DIFFRACTION2B32 - 97

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