+Open data
-Basic information
Entry | Database: PDB / ID: 5ma4 | |||||||||
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Title | GFP-binding DARPin fusion gc_K7 | |||||||||
Components |
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Keywords | FLUORESCENT PROTEIN / green fluorescent protein / designed ankyrin protein | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Aequorea victoria (jellyfish) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Hansen, S. / Stueber, J. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Plueckthun, A. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity. Authors: Hansen, S. / Stuber, J.C. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Pluckthun, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ma4.cif.gz | 331.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ma4.ent.gz | 272.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ma4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/5ma4 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma4 | HTTPS FTP |
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-Related structure data
Related structure data | 5ma3C 5ma5C 5ma6C 5ma8C 5ma9C 5madC 5makC 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: 27453.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P42212 |
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#2: Protein | Mass: 31362.932 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) |
#3: 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: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium Acetate trihydrate, 0.1M TRIS HCl pH 8.5, 30%w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 19, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→47.293 Å / Num. obs: 102263 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.63 |
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.11 / CC1/2: 0.735 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.293 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→47.293 Å
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Refine LS restraints |
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LS refinement shell |
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