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Yorodumi- PDB-3bx9: Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 2.0 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bx9 | ||||||
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Title | Monomeric Far-red Fluorescent Protein mKate Crystallized at pH 2.0 | ||||||
Components | Far-red fluorescent protein mKate | ||||||
Keywords | FLUORESCENT PROTEIN / Far-red fluorescent protein / E. quadricolor / Chromophore structure / pH-induced cis-trans izomerization | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / CITRIC ACID Function and homology information | ||||||
Biological species | Entacmaea quadricolor (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pletnev, S. / Pletneva, N. / Pletnev, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: A Crystallographic Study of Bright Far-Red Fluorescent Protein mKate Reveals pH-induced cis-trans Isomerization of the Chromophore. Authors: Pletnev, S. / Shcherbo, D. / Chudakov, D.M. / Pletneva, N. / Merzlyak, E.M. / Wlodawer, A. / Dauter, Z. / Pletnev, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bx9.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bx9.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/3bx9 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/3bx9 | HTTPS FTP |
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-Related structure data
Related structure data | 3bxaC 3bxbC 3bxcC 1uisS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 27640.482 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) / Strain (production host): XL1 Blue #2: Chemical | ChemComp-CIT / #3: Chemical | #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: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 293 K / pH: 2 Details: 20% w/v PEG 3350, 0.2M ammonium citrate tribasic, 0.4M citric acid, pH 2.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.43 Å / Num. all: 53976 / Num. obs: 52642 / % possible obs: 99.9 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 5.63 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UIS Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.224 / SU ML: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å
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