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- PDB-7bae: Crystal structure of PAFB -

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Basic information

Entry
Database: PDB / ID: 7bae
TitleCrystal structure of PAFB
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / Penicillium chrysogenum antifungal protein B / calix[n]arene / porous framework / zinc
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / host cell cytoplasm / extracellular region / Antifungal protein B
Function and homology information
Biological speciesPenicillium rubens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGuagnini, F. / Huber, A. / Alex, J.M. / Marx, F. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Irish Research CouncilGOIPD/2019/513 Ireland
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Porous assembly of an antifungal protein mediated by zinc and sulfonato-calix[8]arene.
Authors: Guagnini, F. / Huber, A. / Alex, J.M. / Marx, F. / Crowley, P.B.
History
DepositionDec 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifungal protein


Theoretical massNumber of molelcules
Total (without water)6,5161
Polymers6,5161
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.124, 36.953, 24.878
Angle α, β, γ (deg.)90, 103.84, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Antifungal protein


Mass: 6516.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium rubens (strain ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255) (fungus)
Strain: ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255
Gene: afp, Pc12g08290
Production host: Penicillium rubens Wisconsin 54-1255 (fungus)
References: UniProt: B6GXZ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.7 mM Palmitic acid, 0.1 M Potassium phosphate citrate pH 4.2, 40 % PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.2→31.51 Å / Num. obs: 16905 / % possible obs: 98.3 % / Redundancy: 6.7 % / CC1/2: 0.997 / Net I/σ(I): 13.9
Reflection shellResolution: 1.2→1.2 Å / Num. unique obs: 799 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimlessdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HAJ

6haj


Resolution: 1.2→31.5 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.046 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.049 / SU Rfree Blow DPI: 0.049 / SU Rfree Cruickshank DPI: 0.047
RfactorNum. reflection% reflectionSelection details
Rfree0.23 809 -RANDOM
Rwork0.2114 ---
obs0.2123 16905 98.2 %-
Solvent computationVDW probe radii: 11 Å
Displacement parametersBiso mean: 19.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.9793 Å20 Å2-0.7275 Å2
2---1.7117 Å20 Å2
3---0.7323 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.2→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 0 0 54 498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01456HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.04610HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d164SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes78HARMONIC5
X-RAY DIFFRACTIONt_it456HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion55SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact433SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.09
X-RAY DIFFRACTIONt_other_torsion11.3
LS refinement shellResolution: 1.2→1.21 Å
RfactorNum. reflection% reflection
Rfree0.2136 26 -
Rwork0.1918 --
obs0.1931 423 94.04 %
Refinement TLS params.Method: refined / Origin x: 12.0151 Å / Origin y: 8.0073 Å / Origin z: 16.3364 Å
111213212223313233
T0.0011 Å2-0.0059 Å20.0033 Å2--0.0057 Å2-0.0005 Å2---0.0022 Å2
L0.3308 °2-0.5501 °20.1765 °2-0.8338 °20.0943 °2--0.2845 °2
S0.012 Å °-0.045 Å °-0.0249 Å °-0.045 Å °0.0032 Å °-0.0017 Å °-0.0249 Å °-0.0017 Å °-0.0152 Å °
Refinement TLS groupSelection details: { A|-2 - A|55 }

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