+Open data
-Basic information
Entry | Database: PDB / ID: 7zw2 | ||||||
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Title | Penicillium expansum antifungal protein B | ||||||
Components | Antifungal proteinAntifungal protein family | ||||||
Keywords | ANTIFUNGAL PROTEIN / Penicillium expansum / antifungal protein B | ||||||
Function / homology | Antifungal protein / Antifungal protein domain superfamily / Antifungal protein / defense response to fungus / killing of cells of another organism / Antifungal protein Function and homology information | ||||||
Biological species | Penicillium expansum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Gallego del Sol, F. / Marina, A. / Manzanares, P. / Marcos, J.F. / Giner Llorca, M. | ||||||
Funding support | Spain, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zw2.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zw2.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/7zw2 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/7zw2 | HTTPS FTP |
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-Related structure data
Related structure data | 7ztfSC 7ztjC 7zutC 7zvhC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6738.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium expansum (fungus) / References: UniProt: A0A0A2K0J0 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.75 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 400, 0.1M Hepes pH 7.5, 0.2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 21, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.86 Å2 / Biso mean: 16.302 Å2 / Biso min: 4.38 Å2
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Refinement step | Cycle: final / Resolution: 1.2→40.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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