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Open data
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Basic information
Entry | Database: PDB / ID: 7zvh | ||||||
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Title | Penicillium expansum antifungal protein B | ||||||
![]() | Antifungal protein | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gallego del Sol, F. / Marina, A. / Manzanares, P. / Marcos, J.F. / Giner Llorca, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.3 KB | Display | ![]() |
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PDB format | ![]() | 45.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ztfSC ![]() 7ztjC ![]() 7zutC ![]() 7zw2C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 6675.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.19 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium chloride, 0.1 M HEPES pH 7.5, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 22, 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→40.454 Å / Num. all: 17032 / Num. obs: 17032 / % possible obs: 100 % / Redundancy: 8.9 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.078 / Rsym value: 0.074 / Net I/av σ(I): 4.8 / Net I/σ(I): 13.1 / Num. measured all: 151614 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7ZTF Resolution: 1.2→40.45 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.167 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.036 / 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: 60.51 Å2 / Biso mean: 17.378 Å2 / Biso min: 8.91 Å2
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Refinement step | Cycle: final / Resolution: 1.2→40.45 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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