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Yorodumi- PDB-7ax2: Crystal structure of the computationally designed Scone-E protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ax2 | |||||||||||||||
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Title | Crystal structure of the computationally designed Scone-E protein co-crystallized with STA, form b | |||||||||||||||
Components | Scone-E | |||||||||||||||
Keywords | DE NOVO PROTEIN / Beta-propeller / Computational design | |||||||||||||||
Function / homology | Monolacunary Keggin (STA) / Keggin (STA) Function and homology information | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||||||||
Authors | Mylemans, B. / Vandebroek, L. / Parac-Vogt, T.N. / Voet, A.R.D. | |||||||||||||||
Funding support | Belgium, 4items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Crystal structures of Scone: pseudosymmetric folding of a symmetric designer protein. Authors: Mylemans, B. / Killian, T. / Vandebroek, L. / Van Meervelt, L. / Tame, J.R.H. / Parac-Vogt, T.N. / Voet, A.R.D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ax2.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ax2.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ax2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ax2_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7ax2_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7ax2_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7ax2_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/7ax2 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/7ax2 | HTTPS FTP |
-Related structure data
Related structure data | 7awyC 7awzC 7ax0C 6tjgS 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: 40116.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Chemical | ChemComp-SIW / |
#3: Chemical | ChemComp-S5T / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.12 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.9M Sodium malonate 3.5 mM STA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→94.41 Å / Num. obs: 37562 / % possible obs: 100 % / Redundancy: 22.5 % / Biso Wilson estimate: 18.94 Å2 / CC1/2: 0.951 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.077 / Χ2: 0.92 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 23.4 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 3012 / CC1/2: 0.964 / Rpim(I) all: 0.437 / Χ2: 0.89 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TJG Resolution: 2.1→47.21 Å / SU ML: 0.171 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4412 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→47.21 Å
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Refine LS restraints |
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LS refinement shell |
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