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- PDB-6haj: Crystal structure of PAF - p-sulfonatocalix[8]arene complex -

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Basic information

Entry
Database: PDB / ID: 6haj
TitleCrystal structure of PAF - p-sulfonatocalix[8]arene complex
ComponentsPc24g00380 protein
KeywordsANTIFUNGAL PROTEIN / Penicillium chrysogenum / calixarene / molecular glues / nucleating agent
Function / homology
Function and homology information


defense response to fungus
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-7PE / sulfonato-calix[8]arene / Pc24g00380 protein
Similarity search - Component
Biological speciesPenicillium rubens Wisconsin 54-1255 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 2.0Apr 17, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pc24g00380 protein
B: Pc24g00380 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3264
Polymers12,5262
Non-polymers1,8002
Water1,38777
1
A: Pc24g00380 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5732
Polymers6,2631
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pc24g00380 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7532
Polymers6,2631
Non-polymers1,4891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.300, 24.300, 313.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Pc24g00380 protein


Mass: 6263.099 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Penicillium rubens Wisconsin 54-1255 (fungus)
References: UniProt: B6HWK0
#2: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EVB / sulfonato-calix[8]arene


Mass: 1489.481 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H48O32S8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 28 % 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: 1.5→21.06 Å / Num. obs: 16146 / % possible obs: 96.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.037 / Rrim(I) all: 0.089 / Net I/σ(I): 8.4
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2346 / CC1/2: 0.226 / Rpim(I) all: 0.474 / Rrim(I) all: 0.982 / % possible all: 97.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HA4 but devoid of the calixarene
Resolution: 1.5→21.04 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1609 9.97 %RANDOM
Rwork0.217 ---
obs0.22 16146 96.8 %-
Displacement parametersBiso mean: 31.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.2953 Å20 Å20 Å2
2---2.2953 Å20 Å2
3---4.5907 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.5→21.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 117 77 1060
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011872HARMONIC6
X-RAY DIFFRACTIONt_angle_deg1.013361HARMONIC6
X-RAY DIFFRACTIONt_dihedral_angle_d442SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes286HARMONIC5
X-RAY DIFFRACTIONt_it1872HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.03
X-RAY DIFFRACTIONt_other_torsion15.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion122SEMIHARMONIC5
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_contact1997SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.6 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3014 294 9.95 %
Rwork0.2475 2661 -
all0.2529 2955 -
obs--97.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.99050.4374-0.8412.0610.57652.02920.066-0.14560.0599-0.0856-0.0741-0.05420.0527-0.11970.008-0.1226-0.04220.0126-0.09-0.0064-0.1287-8.3955.70360.8487
21.9808-0.3501-1.02271.8151-0.31661.49680.09460.15050.06860.0561-0.08470.09320.01440.1115-0.0099-0.12150.0470.0107-0.0930.0103-0.12718.00335.4473-27.0392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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