+Open data
-Basic information
Entry | Database: PDB / ID: 5ma6 | ||||||
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Title | GFP-binding DARPin 3G124nc | ||||||
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: 2.3 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 | 5ma6.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ma6.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ma6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/5ma6 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/5ma6 | HTTPS FTP |
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-Related structure data
Related structure data | 5ma3C 5ma4C 5ma5C 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: 16965.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria) | ||||
#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-EDO / | #5: 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: 3.48 Å3/Da / Density % sol: 64.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na-Acetate pH 5.5, 0.5M KH2PO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50.01 Å / Num. obs: 29482 / % possible obs: 98.7 % / Redundancy: 37.3 % / CC1/2: 1 / Rmerge(I) obs: 0.148 / Net I/σ(I): 17.55 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 40.7 % / Rmerge(I) obs: 8.52 / Mean I/σ(I) obs: 0.68 / CC1/2: 0.416 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 23.158 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.181 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→50.01 Å
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Refine LS restraints |
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