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- PDB-7bad: Crystal structure of PAFB in complex with p-sulfonato-calix[8]are... -

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Basic information

Entry
Database: PDB / ID: 7bad
TitleCrystal structure of PAFB in complex with p-sulfonato-calix[8]arene and zinc
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / Penicillium chrysogenum antifungal protein B / calix[n]arene / zinc / porous framework / molecular recognition
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / host cell cytoplasm / extracellular region
Similarity search - Function
Antifungal protein / Antifungal protein domain superfamily / Antifungal protein
Similarity search - Domain/homology
sulfonato-calix[8]arene / PHOSPHATE ION / Antifungal protein B
Similarity search - Component
Biological speciesPenicillium rubens
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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: Antifungal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2615
Polymers6,5161
Non-polymers1,7454
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-20 kcal/mol
Surface area5170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.175, 101.175, 46.303
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-103-

PO4

21A-103-

PO4

31A-104-

PO4

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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: 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
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.5 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 40% MPD, 5% PEG 8000

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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: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98013 Å / Relative weight: 1
ReflectionResolution: 1.69→31.82 Å / Num. obs: 10271 / % possible obs: 99.8 % / Redundancy: 18.9 % / Biso Wilson estimate: 27.97 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.056 / Rrim(I) all: 0.224 / Net I/σ(I): 17.9 / Num. measured all: 194217 / Scaling rejects: 8608
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
1.69-1.7818.21.7672723414930.9120.4211.8172.8100
5.34-31.8217.30.06960543500.9960.0170.07142.699.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (18-SEP-2020)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
pointlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HAJ

6haj


Resolution: 1.69→31.82 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.114 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.109
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION. REFINEMENT NOTES. NUMBER OF REFINEMENT NOTES : 1 NOTE 1 : IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 458 4.48 %RANDOM
Rwork0.2291 ---
obs0.231 10227 99.4 %-
Displacement parametersBiso max: 68.94 Å2 / Biso mean: 35.77 Å2 / Biso min: 16.48 Å2
Baniso -1Baniso -2Baniso -3
1-5.289 Å20 Å20 Å2
2--5.289 Å20 Å2
3----10.578 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.69→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 107 49 608
Biso mean--39.04 42.27 -
Num. residues----57
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d190SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes88HARMONIC5
X-RAY DIFFRACTIONt_it576HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion56SEMIHARMONIC5
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_contact459SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d640HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg906HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion18.68
LS refinement shellResolution: 1.69→1.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.2456 17 3.66 %
Rwork0.2487 448 -
all0.2486 465 -
obs--100 %

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