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- PDB-7zw2: Penicillium expansum antifungal protein B -

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Basic information

Entry
Database: PDB / ID: 7zw2
TitlePenicillium expansum antifungal protein B
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / Penicillium expansum / antifungal protein B
Function / homologyAntifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / Antifungal protein
Function and homology information
Biological speciesPenicillium expansum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGallego del Sol, F. / Marina, A. / Manzanares, P. / Marcos, J.F. / Giner Llorca, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Rationally designed antifungal protein chimeras reveal new insights into structure-activity relationship.
Authors: Giner-Llorca, M. / Del Sol, F.G. / Marcos, J.F. / Marina, A. / Manzanares, P.
History
DepositionMay 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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)6,8454
Polymers6,7391
Non-polymers1063
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-10 kcal/mol
Surface area4360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.292, 46.292, 42.366
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Antifungal protein


Mass: 6738.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium expansum (fungus) / References: UniProt: A0A0A2K0J0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.94 Å3/Da / Density % sol: 36.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 400, 0.1M Hepes pH 7.5, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.2→40.09 Å / Num. all: 16814 / Num. obs: 16814 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.092 / Rsym value: 0.087 / Net I/av σ(I): 4.9 / Net I/σ(I): 12.1 / Num. measured all: 148926
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.2-1.266.20.5561.31473023900.2350.6050.5562.599.4
1.26-1.348.70.5091.51978022860.1830.5410.5093.6100
1.34-1.439.40.3522.12027721670.1220.3730.3525.3100
1.43-1.559.50.2422.91918120150.0830.2560.2427.4100
1.55-1.79.60.17541795218640.0590.1850.17510.5100
1.7-1.99.70.1275.41630416870.0430.1350.12714.1100
1.9-2.199.70.0877.11448815010.0290.0910.08720.9100
2.19-2.689.40.0689.31217012920.0230.0720.06826.2100
2.68-3.798.70.05610877910070.020.060.05632.6100
3.79-42.3668.70.04910.552656050.0170.0520.04935.3100

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZTF

7ztf


Resolution: 1.2→40.09 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.159 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 1192 7.1 %RANDOM
Rwork0.137 ---
obs0.1388 15589 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.86 Å2 / Biso mean: 16.302 Å2 / Biso min: 4.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å2-0 Å2
2---0.14 Å20 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.2→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms459 0 3 65 527
Biso mean--12.32 27.79 -
Num. residues----56
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019515
X-RAY DIFFRACTIONr_bond_other_d0.0020.02451
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.946698
X-RAY DIFFRACTIONr_angle_other_deg1.04631069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.888566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72823.46226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39715101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.175154
X-RAY DIFFRACTIONr_chiral_restr0.1080.267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02586
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02106
X-RAY DIFFRACTIONr_rigid_bond_restr2.1743966
X-RAY DIFFRACTIONr_sphericity_free22.421553
X-RAY DIFFRACTIONr_sphericity_bonded8.8435962
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 85 -
Rwork0.23 1123 -
all-1208 -
obs--98.53 %

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