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- PDB-6cs9: Crystal structure of human beta-defensin 2 in complex with PIP2 -

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Basic information

Entry
Database: PDB / ID: 6cs9
TitleCrystal structure of human beta-defensin 2 in complex with PIP2
ComponentsBeta-defensin 4A
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / antifungal / defensin / innate defense
Function / homology
Function and homology information


CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis ...CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Antimicrobial Peptide, Beta-defensin 2; Chain A / Antimicrobial Peptide, Beta-defensin 2; Chain A / Beta defensin type / Beta defensin / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-PIO / Defensin beta 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsJarva, M. / Phan, K. / Lay, F.T. / Humble, C. / Hulett, M. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Sci Adv / Year: 2018
Title: Human beta-defensin 2 killsCandida albicansthrough phosphatidylinositol 4,5-bisphosphate-mediated membrane permeabilization.
Authors: Jarva, M. / Phan, T.K. / Lay, F.T. / Caria, S. / Kvansakul, M. / Hulett, M.D.
History
DepositionMar 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-defensin 4A
B: Beta-defensin 4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1784
Polymers8,6852
Non-polymers1,4932
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.871, 25.538, 40.170
Angle α, β, γ (deg.)90.000, 98.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Beta-defensin 4A / Beta-defensin 2 / hBD-2 / Defensin / beta 2 / Skin-antimicrobial peptide 1 / SAP1


Mass: 4342.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFB4A, DEFB102, DEFB2, DEFB4, DEFB4B / Production host: Komagataella pastoris (fungus) / References: UniProt: O15263
#2: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.38
Details: 0.697M Sodium-malonate-malonic acid, 0.1M glycine-glycine, pH 8.38

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→39.71 Å / Num. obs: 5703 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Net I/σ(I): 10.5 / Num. measured all: 20208
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.892.50.7837423000.5090.6231.011.187
9.06-39.713.20.032199630.9980.0230.0427.799

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.85 Å39.71 Å
Translation1.85 Å39.71 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PHASER2.7.16phasing
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FD4

1fd4


Resolution: 1.85→39.714 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 299 5.25 %RANDOM
Rwork0.1947 5394 --
obs0.1964 5693 97.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.57 Å2 / Biso mean: 36.2562 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 1.85→39.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms598 0 94 28 720
Biso mean--48.87 42.89 -
Num. residues----82
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-2.3310.26021510.23212610276196
2.331-39.72360.21471480.184327842932100

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