+Open data
-Basic information
Entry | Database: PDB / ID: 6hah | |||||||||
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Title | Crystal structure of PAF - p-sulfonatocalix[6]arene complex | |||||||||
Components | Pc24g00380 protein | |||||||||
Keywords | ANTIFUNGAL PROTEIN / Penicillium chrysogenum / calixarene / molecular glues / nucleating agent | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Penicillium rubens Wisconsin 54-1255 (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Alex, J.M. / Rennie, M. / Engilberge, S. / Batta, G. / Crowley, P.B. | |||||||||
Funding support | Ireland, 2items
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Citation | Journal: Iucrj / Year: 2019 Title: Calixarene-mediated assembly of a small antifungal protein. Authors: Alex, J.M. / Rennie, M.L. / Engilberge, S. / Lehoczki, G. / Dorottya, H. / Fizil, A. / Batta, G. / Crowley, P.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hah.cif.gz | 41.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hah.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 6hah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6hah ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6hah | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 6263.099 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Penicillium rubens Wisconsin 54-1255 (fungus) References: UniProt: B6HWK0 |
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-Non-polymers , 5 types, 59 molecules
#2: Chemical | ChemComp-FWQ / |
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#3: Chemical | ChemComp-FWN / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 30% PEG 3350 + 0.05 M Sodium acetate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→27 Å / Num. obs: 8592 / % possible obs: 94.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.042 / Rrim(I) all: 0.074 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 397 / CC1/2: 0.76 / Rpim(I) all: 0.204 / Rrim(I) all: 0.339 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PAF-p-sulfonatocalix[4]arene structure (but devoid of the p-sulfonatocalix[4]arene) Resolution: 1.45→27 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.097 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.091
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Displacement parameters | Biso mean: 24.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.45→27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.62 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 12.4659 Å / Origin y: 7.7242 Å / Origin z: 37.7892 Å
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Refinement TLS group | Selection details: { A|* } |