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- PDB-3lo2: Crystal structure of human alpha-defensin 1 (Y21A mutant) -

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Basic information

Entry
Database: PDB / ID: 3lo2
TitleCrystal structure of human alpha-defensin 1 (Y21A 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 / 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
trifluoroacetic acid / Neutrophil defensin 1
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 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 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)7,1666
Polymers6,7202
Non-polymers4464
Water1,31573
1
A: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,7104
Polymers3,3601
Non-polymers3503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4562
Polymers3,3601
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-34 kcal/mol
Surface area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.675, 29.882, 41.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-72-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 6 / Auth seq-ID: 1 - 30 / Label seq-ID: 1 - 30

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
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: 3360.015 Da / Num. of mol.: 2 / Fragment: UNP residues 65-94 / Mutation: Y21A / Source method: obtained synthetically / Details: Protein is naturally found in HUMAN / References: UniProt: P59665
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 8,000; 0.2 M ammonium sulfate, pH pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: pH 8

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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: Mar 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 3.1 % / Number: 23252 / Rmerge(I) obs: 0.107 / Χ2: 1.2 / D res high: 1.56 Å / D res low: 50 Å / Num. obs: 7547 / % possible obs: 92
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.235087.110.1351.2813
3.364.2390.710.1211.0893.2
2.943.3692.610.11.0083.1
2.672.9492.110.0911.4413.2
2.482.6793.110.0791.1333.1
2.332.4893.210.0691.1013.3
2.212.3394.510.0711.1143.1
2.122.2192.210.0731.1273.1
2.042.1293.410.0761.1193.2
1.972.0494.410.0681.0553.1
1.91.9793.410.0681.0443.1
1.851.992.810.0691.2183
1.81.859310.0741.3673
1.761.893.110.0771.2583.1
1.721.7693.510.0761.1373
1.681.729510.0841.2443
1.651.6891.510.0791.3683
1.621.6593.810.0851.2683
1.591.6290.810.0921.4523.1
1.561.5980.310.1061.2532.9
ReflectionResolution: 1.56→41.552 Å / Num. all: 8139 / Num. obs: 7534 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.107 / Rsym value: 0.157 / Net I/σ(I): 10.3
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.11 / % possible all: 80.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GNY

3gny


Resolution: 1.56→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.754 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19966 341 4.5 %RANDOM
Rwork0.17334 ---
obs0.17458 7190 92.63 %-
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: 13.388 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms462 0 28 73 563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.671.987681
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.695558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.8741820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8171570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.709158
X-RAY DIFFRACTIONr_chiral_restr0.1150.266
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021370
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_it0.8791.5298
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3712468
X-RAY DIFFRACTIONr_scbond_it2.4313203
X-RAY DIFFRACTIONr_scangle_it3.8884.5213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 231 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.545
loose thermal1.8810
LS refinement shellResolution: 1.562→1.602 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 27 -
Rwork0.177 500 -
obs--90.55 %
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)
12.12830.7280.3850.6251-0.10690.45090.0062-0.11160.0338-0.0004-0.010.06320.0102-0.03990.00380.04390.00240.00460.080.00020.107310.1888-1.1121-6.0054
21.1682-1.20360.14165.05980.42421.38980.02150.0972-0.0006-0.1363-0.0270.1311-0.0632-0.03740.00550.06490.0047-0.00510.07010.00110.084713.73628.3376-14.1346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30

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