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- PDB-9iid: Crystal structure of PgAfp -

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Basic information

Entry
Database: PDB / ID: 9iid
TitleCrystal structure of PgAfp
ComponentsAntifungal protein B
KeywordsANTIMICROBIAL PROTEIN / PgAFP
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / host cell cytoplasm / extracellular region / Antifungal protein B
Function and homology information
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2025
Title: The role of Npt1 in regulating antifungal protein activity in filamentous fungi.
Authors: Wang, Y. / Wang, S. / Chen, Y. / Xie, C. / Xu, H. / Lin, Y. / Lin, R. / Zeng, W. / Chen, X. / Nie, X. / Wang, S.
History
DepositionJun 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antifungal protein B


Theoretical massNumber of molelcules
Total (without water)6,6711
Polymers6,6711
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.760, 61.760, 42.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-151-

HOH

21A-152-

HOH

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Components

#1: Protein Antifungal protein B


Mass: 6670.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: pafB / Production host: Escherichia coli (E. coli) / References: UniProt: D0EXD3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.31 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: pH8.0, 3.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→22.56 Å / Num. obs: 5627 / % possible obs: 98.08 % / Redundancy: 8.3 % / CC1/2: 0.999 / Net I/σ(I): 57.92
Reflection shellResolution: 1.78→1.844 Å / Num. unique obs: 489 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→22.56 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 2.38 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 283 5.03 %
Rwork0.172 --
obs0.1741 5627 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→22.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms451 0 0 72 523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.938
X-RAY DIFFRACTIONf_dihedral_angle_d4.1361
X-RAY DIFFRACTIONf_chiral_restr0.0663
X-RAY DIFFRACTIONf_plane_restr0.00580
LS refinement shellResolution: 1.78→1.84 Å
RfactorNum. reflection% reflection
Rfree0.175 125 -
Rwork0.1543 2634 -
obs--96 %

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