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- PDB-7zut: Penicillium expansum chimera loop1 -

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Basic information

Entry
Database: PDB / ID: 7zut
TitlePenicillium expansum chimera loop1
ComponentsAntifungal protein
KeywordsANTIFUNGAL PROTEIN / Penicillium expansum / chimeric
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: 1.1 Å
AuthorsGallego, 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 13, 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)6,9495
Polymers6,6861
Non-polymers2634
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-24 kcal/mol
Surface area4200 Å2
Unit cell
Length a, b, c (Å)44.931, 44.931, 42.829
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

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Components

#1: Protein Antifungal protein


Mass: 6685.502 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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 3.5M ammonium sulphate, 1% MPD, 0.1M Mes pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→42.83 Å / Num. obs: 20337 / % possible obs: 98 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.012 / Net I/σ(I): 40.8
Reflection shellResolution: 1.1→1.16 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 2596 / Rpim(I) all: 0.035

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Processing

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

7ztf


Resolution: 1.1→38.91 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.577 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1459 1093 5.4 %RANDOM
Rwork0.1259 ---
obs0.127 19218 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.25 Å2 / Biso mean: 12.202 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 1.1→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms455 0 12 70 537
Biso mean--18.41 23.03 -
Num. residues----57
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.019530
X-RAY DIFFRACTIONr_bond_other_d0.0020.02470
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.959723
X-RAY DIFFRACTIONr_angle_other_deg0.87431117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.901570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.412425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8315107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.708153
X-RAY DIFFRACTIONr_chiral_restr0.0980.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0298
X-RAY DIFFRACTIONr_rigid_bond_restr0.84131000
X-RAY DIFFRACTIONr_sphericity_free19.08544
X-RAY DIFFRACTIONr_sphericity_bonded5.61351010
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.127 56 -
Rwork0.105 1181 -
all-1237 -
obs--80.96 %

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