+Open data
-Basic information
Entry | Database: PDB / ID: 7aon | ||||||
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Title | Crystal structure of CI2 double mutant L49I,I57V | ||||||
Components | Subtilisin-chymotrypsin inhibitor-2A | ||||||
Keywords | PROTEIN BINDING / Protease inhibitor | ||||||
Function / homology | Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / response to wounding / serine-type endopeptidase inhibitor activity / Subtilisin-chymotrypsin inhibitor-2A Function and homology information | ||||||
Biological species | Hordeum vulgare (barley) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Olsen, J.G. / Teilum, K. / Hamborg, L. / Roche, J.V. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Commun Biol / Year: 2021 Title: Synergistic stabilization of a double mutant in chymotrypsin inhibitor 2 from a library screen in E. coli. Authors: Hamborg, L. / Granata, D. / Olsen, J.G. / Roche, J.V. / Pedersen, L.E. / Nielsen, A.T. / Lindorff-Larsen, K. / Teilum, K. #1: Journal: Biorxiv / Year: 2020 Title: Synergistic stabilization of a double mutant in CI2 from an in-cell library screen Authors: Hamborg, L. / Granata, D. / Olsen, J.G. / Roche, J.V. / Pedersen, L.E. / Nielsen, A.T. / Lindorff-Larsen, K. / Teilum, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aon.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aon.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 7aon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aon_validation.pdf.gz | 261 KB | Display | wwPDB validaton report |
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Full document | 7aon_full_validation.pdf.gz | 261.9 KB | Display | |
Data in XML | 7aon_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 7aon_validation.cif.gz | 4.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/7aon ftp://data.pdbj.org/pub/pdb/validation_reports/ao/7aon | HTTPS FTP |
-Related structure data
Related structure data | 7a1hC 7a3mC 7aokSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7299.596 Da / Num. of mol.: 1 / Mutation: L49I, I57V Source method: isolated from a genetically manipulated source Details: CI-2 double mutant L49I, I57V / Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01053 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.32 Å3/Da / Density % sol: 47 % / Description: Beautiful thick hexagonal plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 40 % (NH4)2SO4, 50 mM Tris-HCl, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.262→59.229 Å / Num. obs: 15866 / % possible obs: 94.7 % / Redundancy: 36.03 % / CC1/2: 0.9995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.016 / Rrim(I) all: 0.094 / Net I/σ(I): 22.585 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AOK Resolution: 1.3→52.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.12 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.061 / 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: 85.56 Å2 / Biso mean: 24.235 Å2 / Biso min: 11.19 Å2
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Refinement step | Cycle: final / Resolution: 1.3→52.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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