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Yorodumi- PDB-3u0n: Crystal structure of the engineered fluorescent protein mRuby, cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u0n | ||||||
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Title | Crystal structure of the engineered fluorescent protein mRuby, crystal form 2 | ||||||
Components | mRuby | ||||||
Keywords | FLUORESCENT PROTEIN | ||||||
Function / homology | Green fluorescent protein-related / Green fluorescent protein / bioluminescence / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta / Red fluorescent protein eqFP611 Function and homology information | ||||||
Biological species | Entacmaea quadricolor (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Akerboom, J. / Looger, L.L. / Schreiter, E.R. | ||||||
Citation | Journal: Front Mol Neurosci / Year: 2013 Title: Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / ...Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / Fischer, E. / Schuler, C. / Chen, T.W. / Sarkisyan, K.S. / Marvin, J.S. / Bargmann, C.I. / Kim, D.S. / Kugler, S. / Lagnado, L. / Hegemann, P. / Gottschalk, A. / Schreiter, E.R. / Looger, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u0n.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u0n.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 3u0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u0n_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 3u0n_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 3u0n_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 3u0n_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/3u0n ftp://data.pdbj.org/pub/pdb/validation_reports/u0/3u0n | HTTPS FTP |
-Related structure data
Related structure data | 3u0kC 3u0lC 3u0mC 4i2yC 1uisS 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
#1: Protein | Mass: 25807.447 Da / Num. of mol.: 1 / Mutation: D196S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ISF8*PLUS | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | MRUBY IS THE ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2.0 M Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 2, 2010 |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→27.9 Å / Num. all: 33021 / Num. obs: 32955 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.69 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1UIS Resolution: 1.6→27.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.228 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 11.722 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→27.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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