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Yorodumi- PDB-5ukg: Crystal Structure of the genetically encoded calcium indicator K-GECO -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ukg | ||||||
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Title | Crystal Structure of the genetically encoded calcium indicator K-GECO | ||||||
Components | K-GECO | ||||||
Keywords | FLUORESCENT PROTEIN / calcium indicator fluorescent protein | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta Function and homology information | ||||||
Biological species | Entacmaea quadricolor (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.36 Å | ||||||
Authors | Schreiter, E.R. | ||||||
Citation | Journal: BMC Biol. / Year: 2018 Title: A genetically encoded Ca2+indicator based on circularly permutated sea anemone red fluorescent protein eqFP578. Authors: Shen, Y. / Dana, H. / Abdelfattah, A.S. / Patel, R. / Shea, J. / Molina, R.S. / Rawal, B. / Rancic, V. / Chang, Y.F. / Wu, L. / Chen, Y. / Qian, Y. / Wiens, M.D. / Hambleton, N. / Ballanyi, ...Authors: Shen, Y. / Dana, H. / Abdelfattah, A.S. / Patel, R. / Shea, J. / Molina, R.S. / Rawal, B. / Rancic, V. / Chang, Y.F. / Wu, L. / Chen, Y. / Qian, Y. / Wiens, M.D. / Hambleton, N. / Ballanyi, K. / Hughes, T.E. / Drobizhev, M. / Kim, D.S. / Koyama, M. / Schreiter, E.R. / Campbell, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ukg.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ukg.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ukg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/5ukg ftp://data.pdbj.org/pub/pdb/validation_reports/uk/5ukg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 46663.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-CA / #3: 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: 2.21 Å3/Da / Density % sol: 44.41 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→75.56 Å / Num. obs: 30298 / % possible obs: 94.6 % / Redundancy: 4.8 % / Net I/σ(I): 5.1 |
-Processing
Software |
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Refinement | Resolution: 2.36→75.56 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.887 / SU B: 12.555 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.651 / ESU R Free: 0.316 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.54 Å2
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Refinement step | Cycle: 1 / Resolution: 2.36→75.56 Å
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Refine LS restraints |
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