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- PDB-6ha4: Crystal structure of PAF - p-sulfonatocalix[4]arene complex -

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Basic information

Entry
Database: PDB / ID: 6ha4
TitleCrystal structure of PAF - p-sulfonatocalix[4]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
Chem-T3Y / Pc24g00380 protein
Similarity search - Component
Biological speciesPenicillium rubens
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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 1.2Jan 17, 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 6, 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)7,1003
Polymers6,2631
Non-polymers8372
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-0 kcal/mol
Surface area4390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.719, 37.587, 29.956
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pc24g00380 protein


Mass: 6263.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Penicillium rubens (strain ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255) (fungus)
References: UniProt: B6HWK0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-T3Y / 25,26,27,28-tetrahydroxypentacyclo[19.3.1.1~3,7~.1~9,13~.1~15,19~]octacosa-1(25),3(28),4,6,9(27),10,12,15(26),16,18,21,23-dodecaene-5,11,17,23-tetrasulfonic acid / 5,11,17,23-tetra-sulphonato-calix[4]arene-25,26,27,28-tetrol


Mass: 744.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24O16S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.9 Å3/Da / Density % sol: 35.15 %
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: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→27.8 Å / Num. obs: 10142 / % possible obs: 92.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.37 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.062 / Rrim(I) all: 0.012 / Net I/av σ(I): 6.1 / Net I/σ(I): 6.1
Reflection shellResolution: 1.33→1.37 Å / Mean I/σ(I) obs: 1.3 / CC1/2: 0.34 / Rpim(I) all: 0.34 / Rrim(I) all: 0.61

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MHV

2mhv


Resolution: 1.33→27.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.069
RfactorNum. reflection% reflectionSelection details
Rfree0.217 526 5.19 %RANDOM
Rwork0.185 ---
obs0.186 10142 92.5 %-
Displacement parametersBiso mean: 20.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.2438 Å20 Å20.718 Å2
2---5.4036 Å20 Å2
3---3.1597 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: 1 / Resolution: 1.33→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms433 0 54 55 542
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.005972HARMONIC6
X-RAY DIFFRACTIONt_angle_deg0.741759HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d230SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes153HARMONIC5
X-RAY DIFFRACTIONt_it972HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.9
X-RAY DIFFRACTIONt_other_torsion17.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion64SEMIHARMONIC5
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_contact1154SEMIHARMONIC4
LS refinement shellResolution: 1.33→1.48 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2254 133 4.96 %
Rwork0.208 2546 -
all0.2089 2679 -
obs--86.77 %
Refinement TLS params.Method: refined / Origin x: -3.7966 Å / Origin y: 4.5228 Å / Origin z: 31.3802 Å
111213212223313233
T-0.0129 Å20.007 Å2-0.0213 Å2--0.0297 Å2-0.0182 Å2---0.0202 Å2
L1.1555 °2-0.1822 °20.0215 °2-0.7064 °2-0.2874 °2--1.1753 °2
S0.0249 Å °0.0048 Å °-0.0542 Å °-0.0008 Å °-0.07 Å °0.0213 Å °-0.0123 Å °-0.0299 Å °0.0452 Å °
Refinement TLS groupSelection details: { A|* }

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