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- PDB-3lo9: Crystal structure of human alpha-defensin 1 (W26Ahp mutant) -

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Basic information

Entry
Database: PDB / ID: 3lo9
TitleCrystal structure of human alpha-defensin 1 (W26Ahp 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
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 / struct_ref_seq_dif
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
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


Theoretical massNumber of molelcules
Total (without water)6,7862
Polymers6,7862
Non-polymers00
Water1,11762
1
A: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)3,3931
Polymers3,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)3,3931
Polymers3,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-8 kcal/mol
Surface area4150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.146, 30.645, 39.820
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
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: 3393.085 Da / Num. of mol.: 2 / Fragment: UNP residues 65-94 / Mutation: W26Ahp / Source method: obtained synthetically / Details: Protein naturally occurs in HUMAN / References: UniProt: P59665
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate trihydrate pH 6.5; 0.2 M sodium citrate tribasic dehydrate; 30% isopropanol , 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: Oct 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.56→30.643 Å / Num. all: 8440 / Num. obs: 8232 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.059 / Rsym value: 0.081 / Net I/σ(I): 20.7
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 18.8 / Num. unique all: 737 / Rsym value: 0.141 / % possible all: 88.2

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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→15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.411 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 383 4.7 %RANDOM
Rwork0.19 ---
obs0.191 8220 97.58 %-
all-7837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.57 Å2 / Biso mean: 12.556 Å2 / Biso min: 4.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.56→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms466 0 0 62 528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022476
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.993634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.929554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.5621820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5231570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.653158
X-RAY DIFFRACTIONr_chiral_restr0.110.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021350
X-RAY DIFFRACTIONr_mcbond_it1.0161.5292
X-RAY DIFFRACTIONr_mcangle_it1.7122454
X-RAY DIFFRACTIONr_scbond_it2.6783184
X-RAY DIFFRACTIONr_scangle_it4.1864.5180
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 233 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.635
LOOSE THERMAL1.8910
LS refinement shellResolution: 1.563→1.603 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 25 -
Rwork0.208 539 -
all-564 -
obs--93.69 %
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)
11.6775-1.2056-0.00674.3481-0.17192.9424-0.04890.1247-0.1798-0.0397-0.04130.5889-0.1202-0.37720.09020.10930.012400.1579-0.02480.1801-14.59338.3887-14.105
25.36251.7985-0.38053.9050.92883.3288-0.0711-0.11110.1830.14880.10520.2579-0.0457-0.1407-0.03410.07920.01290.01290.08890.02360.066-11.0618-1.2368-5.8357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30

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