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- PDB-7baf: Crystal structure of PAFB in complex with zinc -

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Basic information

Entry
Database: PDB / ID: 7baf
TitleCrystal structure of PAFB in complex with zinc
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / Penicillium chrysogenum antifungal protein B / calix[n]arene / zinc / porous framework / molecular recognition
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / host cell cytoplasm / extracellular region / ACETATE ION / Antifungal protein B
Function and homology information
Biological speciesPenicillium rubens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.123 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 / Item: _pdbx_entry_details.has_protein_modification

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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)7,0089
Polymers6,5161
Non-polymers4918
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-67 kcal/mol
Surface area4090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.942, 32.942, 42.825
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 25 % PEG 3350, 0.2 M NH4CH3COO

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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: 1.12→28.53 Å / Num. obs: 19859 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 7.96 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.055 / Rrim(I) all: 0.172 / Net I/σ(I): 10.4 / Num. measured all: 186816 / Scaling rejects: 1456
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
1.12-1.187.31.0142122628940.6910.4051.0952.699.5
3.55-28.539.80.11662056310.9910.0380.1222399.9

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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: 1.123→28.53 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.035 / SU Rfree Blow DPI: 0.034 / SU Rfree Cruickshank DPI: 0.033
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
Rfree0.1852 952 4.82 %RANDOM
Rwork0.1816 ---
obs0.1818 19755 99.5 %-
Displacement parametersBiso max: 37.1 Å2 / Biso mean: 13.04 Å2 / Biso min: 5.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.3681 Å20 Å20 Å2
2---1.3681 Å20 Å2
3---2.7363 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: final / Resolution: 1.123→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms444 0 23 48 515
Biso mean--15.08 18.32 -
Num. residues----57
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d165SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes84HARMONIC5
X-RAY DIFFRACTIONt_it471HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion55SEMIHARMONIC5
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_contact461SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d477HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg638HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion13
LS refinement shellResolution: 1.123→1.13 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2352 24 5.7 %
Rwork0.2008 397 -
obs--86.85 %
Refinement TLS params.Method: refined / Origin x: -1.713 Å / Origin y: 24.3568 Å / Origin z: 11.5421 Å
111213212223313233
T-0.0084 Å20.0088 Å20.0005 Å2--0.0102 Å2-0.002 Å2--0.0073 Å2
L0.0124 °2-0.1108 °2-0.2358 °2-0.3464 °2-0.1921 °2--1.0528 °2
S-0.0069 Å °-0.0078 Å °-0.0046 Å °-0.0139 Å °0.0453 Å °-0.0069 Å °-0.0512 Å °-0.0192 Å °-0.0384 Å °
Refinement TLS groupSelection details: { A|* }

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