+Open data
-Basic information
Entry | Database: PDB / ID: 5knh | ||||||
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Title | CRYSTAL STRUCTURE OF DARPIN 6G9 IN COMPLEX WITH CYNO IL-13 | ||||||
Components |
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Keywords | CYTOKINE/DE NOVO PROTEIN / ALTERNATIVE SCAFFOLD / CYTOKINE-DE NOVO PROTEIN complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | synthetic construct (others) Macaca fascicularis (crab-eating macaque) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Teplyakov, A. / Malia, T. / Obmolova, G. / Gilliland, G. | ||||||
Citation | Journal: Protein Eng. Des. Sel. / Year: 2017 Title: Conformational flexibility of an anti-IL-13 DARPin. Authors: Teplyakov, A. / Malia, T.J. / Obmolova, G. / Jacobs, S.A. / O'Neil, K.T. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5knh.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5knh.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 5knh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/5knh ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5knh | HTTPS FTP |
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-Related structure data
Related structure data | 5kngC 3l5xS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18244.361 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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#2: Protein | Mass: 12302.288 Da / Num. of mol.: 1 / Fragment: UNP residues 22-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca fascicularis (crab-eating macaque) Gene: IL13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0PW92 |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.01 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 11% PEG 3350, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5 PH range: 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 32998 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.7 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L5X Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.299 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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