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- PDB-3lo6: Crystal structure of human alpha-defensin 1 (W26Aba mutant) -

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Basic information

Entry
Database: PDB / ID: 3lo6
TitleCrystal structure of human alpha-defensin 1 (W26Aba 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / 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
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: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)6,8915
Polymers6,7022
Non-polymers1893
Water1,45981
1
A: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)3,3511
Polymers3,3511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,5404
Polymers3,3511
Non-polymers1893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-35 kcal/mol
Surface area4270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.600, 31.024, 39.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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

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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: 3351.006 Da / Num. of mol.: 2 / Fragment: UNP residues 65-94 / Mutation: W26Aba / Source method: obtained synthetically / Details: Protein naturally occurs in HUMAN / References: UniProt: P59665
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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.: 81 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% MPD; 0.1 M HEPES sodium pH 7.5; 0.2 M sodium citrate dihydrate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Feb 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→39.726 Å / Num. all: 8427 / Num. obs: 8416 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.05 / Rsym value: 0.063 / Net I/σ(I): 24.9
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 25 / Num. unique all: 776 / Rsym value: 0.105 / % possible all: 94.4

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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: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.918 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 390 4.6 %RANDOM
Rwork0.169 ---
all0.169 8019 --
obs0.17 8409 99.89 %-
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 max: 60.31 Å2 / Biso mean: 13.777 Å2 / Biso min: 5.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms460 0 10 81 551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022499
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.977676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.361562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.07717.27322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0861578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9361510
X-RAY DIFFRACTIONr_chiral_restr0.1120.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021384
X-RAY DIFFRACTIONr_mcbond_it0.9281.5302
X-RAY DIFFRACTIONr_mcangle_it1.5392478
X-RAY DIFFRACTIONr_scbond_it2.1053197
X-RAY DIFFRACTIONr_scangle_it3.5314.5196
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 214 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.325
LOOSE THERMAL2.4610
LS refinement shellResolution: 1.563→1.603 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 30 -
Rwork0.17 573 -
all-603 -
obs--98.85 %
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)
12.3889-0.8654-0.49993.58790.59812.2889-0.01150.06970.0421-0.0581-0.0026-0.1238-0.00840.05060.01410.03040.0041-0.00930.0276-0.00160.01048.0946-8.1854-13.9239
24.07212.42720.10543.2597-0.6352.107-0.05910.0907-0.17270.02770.1176-0.23550.06110.1014-0.05850.02370.01230.00040.0337-0.02420.032811.59631.397-5.9731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30

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