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- PDB-6hah: Crystal structure of PAF - p-sulfonatocalix[6]arene complex -

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Basic information

Entry
Database: PDB / ID: 6hah
TitleCrystal structure of PAF - p-sulfonatocalix[6]arene complex
ComponentsPc24g00380 protein
KeywordsANTIFUNGAL PROTEIN / Penicillium chrysogenum / calixarene / molecular glues / nucleating agent
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism
Similarity search - Function
Antifungal protein domain / Antifungal protein / Antifungal protein domain superfamily / Antifungal protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2-[2-(2-ethoxyethoxy)ethoxy]ethanol / p-sulfonatocalix[6]arene / Pc24g00380 protein
Similarity search - Component
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsAlex, J.M. / Rennie, M. / Engilberge, S. / Batta, G. / Crowley, P.B.
Funding support Ireland, 2items
OrganizationGrant numberCountry
Science Foundation Ireland13/CDA/2168 Ireland
Science Foundation Ireland13/ERC/B2912 Ireland
CitationJournal: Iucrj / Year: 2019
Title: Calixarene-mediated assembly of a small antifungal protein.
Authors: Alex, J.M. / Rennie, M.L. / Engilberge, S. / Lehoczki, G. / Dorottya, H. / Fizil, A. / Batta, G. / Crowley, P.B.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 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 1.3Oct 23, 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: Pc24g00380 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6675
Polymers6,2631
Non-polymers1,4044
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-8 kcal/mol
Surface area4680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.739, 38.590, 29.230
Angle α, β, γ (deg.)90.00, 112.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pc24g00380 protein


Mass: 6263.099 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Penicillium rubens Wisconsin 54-1255 (fungus)
References: UniProt: B6HWK0

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Non-polymers , 5 types, 59 molecules

#2: Chemical ChemComp-FWQ / p-sulfonatocalix[6]arene


Mass: 1111.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H30O24S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FWN / 2-[2-(2-ethoxyethoxy)ethoxy]ethanol


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 30% PEG 3350 + 0.05 M Sodium acetate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→27 Å / Num. obs: 8592 / % possible obs: 94.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.042 / Rrim(I) all: 0.074 / Net I/σ(I): 11.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 397 / CC1/2: 0.76 / Rpim(I) all: 0.204 / Rrim(I) all: 0.339 / % possible all: 90.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PAF-p-sulfonatocalix[4]arene structure (but devoid of the p-sulfonatocalix[4]arene)

Resolution: 1.45→27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.236 440 5.13 %RANDOM
Rwork0.2 ---
obs0.202 8576 94.2 %-
Displacement parametersBiso mean: 24.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.7307 Å20 Å2-0.8092 Å2
2---0.9853 Å20 Å2
3---2.716 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.45→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms433 0 91 55 579
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.009993HARMONIC6
X-RAY DIFFRACTIONt_angle_deg11776HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d236SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes151HARMONIC5
X-RAY DIFFRACTIONt_it993HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.36
X-RAY DIFFRACTIONt_other_torsion17.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion62SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1175SEMIHARMONIC4
LS refinement shellResolution: 1.45→1.62 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2405 133 5.58 %
Rwork0.2043 2251 -
all0.2065 2384 -
obs--92.53 %
Refinement TLS params.Method: refined / Origin x: 12.4659 Å / Origin y: 7.7242 Å / Origin z: 37.7892 Å
111213212223313233
T-0.0226 Å2-0.0093 Å2-0.0254 Å2--0.0047 Å20.0059 Å2---0.0152 Å2
L2.5255 °22.949 °2-0.6422 °2-9.4775 °2-1.4472 °2--3.8355 °2
S-0.1803 Å °-0.0181 Å °-0.0198 Å °-0.4821 Å °0.156 Å °0.0334 Å °0.1075 Å °0.0473 Å °0.0242 Å °
Refinement TLS groupSelection details: { A|* }

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