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

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Basic information

Entry
Database: PDB / ID: 7ztf
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: 1.1 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 10, 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)6,8385
Polymers6,7081
Non-polymers1294
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-23 kcal/mol
Surface area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.332, 46.332, 42.089
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-279-

HOH

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Components

#1: Protein Antifungal protein


Mass: 6708.495 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.96 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 30% jeffamine M60C, 10% DMSO

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Data collection

DiffractionMean temperature: 83 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.1→40.125 Å / Num. all: 21626 / Num. obs: 21626 / % possible obs: 100 % / Redundancy: 15.6 % / Rpim(I) all: 0.017 / Rrim(I) all: 0.065 / Rsym value: 0.063 / Net I/av σ(I): 4.3 / Net I/σ(I): 40.1 / Num. measured all: 337920
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs
1.1-1.1615.20.0778.14739031120.020.0790.07730.5
1.16-1.2315.20.0669.44466529380.0180.0690.06634.2
1.23-1.3116.10.0659.24469227800.0170.0670.06536.5
1.31-1.4215.30.069.73950125800.0160.0620.0638.7
1.42-1.5616.40.058103919123920.0150.060.05842.8
1.56-1.7416.30.0589.83547121810.0150.060.05845.5
1.74-2.01150.0589.42911819450.0150.060.05845.6
2.01-2.4616.50.0599.32697316350.0150.0610.05949.6
2.46-3.48150.0628.11945113000.0170.0640.06248
3.48-42.089150.0717.5114687630.0190.0730.07148.1

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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: 6ha4

6ha4


Resolution: 1.1→40.12 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.491 / SU ML: 0.011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1383 1062 4.9 %RANDOM
Rwork0.1161 ---
obs0.1172 20536 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.11 Å2 / Biso mean: 9.15 Å2 / Biso min: 2.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å2-0 Å2
2---0.2 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 1.1→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms457 0 4 89 550
Biso mean--10.01 19.99 -
Num. residues----57
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019526
X-RAY DIFFRACTIONr_bond_other_d0.0020.02489
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.945714
X-RAY DIFFRACTIONr_angle_other_deg1.00431166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.6842425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6615115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.253153
X-RAY DIFFRACTIONr_chiral_restr0.1040.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0298
X-RAY DIFFRACTIONr_rigid_bond_restr9.48931015
X-RAY DIFFRACTIONr_sphericity_free19.957560
X-RAY DIFFRACTIONr_sphericity_bonded8.47751027
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.113 68 -
Rwork0.105 1492 -
all-1560 -
obs--100 %

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