+Open data
-Basic information
Entry | Database: PDB / ID: 8oig | |||||||||
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Title | Crystal Structure of Staphopain C from Staphylococcus aureus | |||||||||
Components | Thiol proteaseCysteine protease | |||||||||
Keywords | HYDROLASE / cystein protease / thiol protease / papain-fold / staphopain | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | |||||||||
Authors | McEwen, A.G. / Magoch, M. / Napolitano, V. / Dubin, G. / Wladyka, B. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Molecules / Year: 2023 Title: Crystal Structure of Staphopain C from Staphylococcus aureus. Authors: Magoch, M. / McEwen, A.G. / Napolitano, V. / Wladyka, B. / Dubin, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oig.cif.gz | 218.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oig.ent.gz | 178.6 KB | Display | PDB format |
PDBx/mmJSON format | 8oig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/8oig ftp://data.pdbj.org/pub/pdb/validation_reports/oi/8oig | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19636.686 Da / Num. of mol.: 3 / Mutation: D101G / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q8RJP3 #2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.5 M AmSO4, 0.1M Tris, ph 8.5, 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.05 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→51.57 Å / Num. obs: 80816 / % possible obs: 97.59 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.07 |
Reflection shell | Resolution: 1.582→1.639 Å / Num. unique obs: 8329 / CC1/2: 0.978 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→51.57 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.322 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.008 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.511 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→51.57 Å
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Refine LS restraints |
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