+Open data
-Basic information
Entry | Database: PDB / ID: 3e5t | ||||||
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Title | Crystal Structure Analysis of FP611 | ||||||
Components | Red fluorescent protein eqFP611 | ||||||
Keywords | FLUORESCENT PROTEIN / Chromophore / Luminescence / Photoprotein / red fluorescent protein | ||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / 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 / molecular replacement / Resolution: 1.1 Å | ||||||
Authors | Nar, H. / Nienhaus, K. / Nienhaus, U. / Wiedenmann, J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611. Authors: Nienhaus, K. / Nar, H. / Heilker, R. / Wiedenmann, J. / Nienhaus, G.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e5t.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e5t.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/3e5t ftp://data.pdbj.org/pub/pdb/validation_reports/e5/3e5t | HTTPS FTP |
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-Related structure data
Related structure data | 3e5vC 3e5wC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27634.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entacmaea quadricolor (sea anemone) Description: synonymous source organism name Parasicyonis actinostoloides Production host: Escherichia coli (E. coli) / Strain (production host): M15pREP4 / References: UniProt: Q8ISF8 |
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#2: 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: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 8000, pH 4.6, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→10 Å / Num. all: 87481 / Num. obs: 71928 / % possible obs: 92.6 % / Observed criterion σ(F): 4 / Rmerge(I) obs: 0.048 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.1→1.14 Å / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3 / % possible all: 82.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UIS Resolution: 1.1→10 Å / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 115.95 Å2 / Biso mean: 22.821 Å2 / Biso min: 7.64 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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