+Open data
-Basic information
Entry | Database: PDB / ID: 5ma9 | |||||||||
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Title | GFP-binding DARPin fusion gc_R11 | |||||||||
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: 1.57 Å | |||||||||
Authors | Hansen, S. / Stueber, J. / Ernst, P. / Koch, A. / Bojar, D. / Batyuk, A. / Plueckthun, A. | |||||||||
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 | 5ma9.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ma9.ent.gz | 997.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ma9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/5ma9 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma9 | HTTPS FTP |
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-Related structure data
Related structure data | 5ma3C 5ma4C 5ma5C 5ma6C 5ma8C 5madC 5makC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27453.949 Da / Num. of mol.: 4 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 #2: Protein | Mass: 31974.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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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: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.5, 30% w/v PEG 4000, 0.2 M LiSO4 |
-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: 1.57→44.682 Å / Num. obs: 302440 / % possible obs: 95.18 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.03 |
Reflection shell | Resolution: 1.57→1.61 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.6 / Num. unique all: 22310 / CC1/2: 0.754 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→44.682 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→44.682 Å
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Refine LS restraints |
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LS refinement shell |
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