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Yorodumi- PDB-6qb2: Crystal structure of the cystatin-based engineered protein scaffo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qb2 | ||||||
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Title | Crystal structure of the cystatin-based engineered protein scaffold SQT-1C | ||||||
Components | Monomer of SQT-1C | ||||||
Keywords | DE NOVO PROTEIN / Engineered Scaffold protein | ||||||
Function / homology | Nuclear Transport Factor 2; Chain: A, - #10 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Levy, C.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Sci Rep / Year: 2019 Title: Studies of the oligomerisation mechanism of a cystatin-based engineered protein scaffold. Authors: Zalar, M. / Indrakumar, S. / Levy, C.W. / Tunnicliffe, R.B. / Peters, G.H.J. / Golovanov, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qb2.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qb2.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/6qb2 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/6qb2 | HTTPS FTP |
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-Related structure data
Related structure data | 3k9mS S: Starting model for refinement |
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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: 15321.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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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: 3.12 Å3/Da / Density % sol: 60.53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 38% Dioxane / Temp details: cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.99 Å / Num. obs: 5209 / % possible obs: 99.79 % / Redundancy: 11.9 % / Biso Wilson estimate: 84.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Net I/σ(I): 17.39 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 497 / CC1/2: 0.685 / Rpim(I) all: 0.27 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K9M Resolution: 2.5→42.99 Å / SU ML: 0.3765 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 28.5026
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 46.0228387245 Å / Origin y: 21.4256424397 Å / Origin z: 0.780314274909 Å
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Refinement TLS group | Selection details: all |