+Open data
-Basic information
Entry | Database: PDB / ID: 5h88 | ||||||
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Title | Crystal structure of mRojoA mutant - T16V -P63F - W143A - L163V | ||||||
Components | mRojoA fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / quantum yield / protein engineering | ||||||
Function / homology | Function and homology information bioluminescence / generation of precursor metabolites and energy / metal ion binding Similarity search - Function | ||||||
Biological species | Discosoma sp. (sea anemone) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.06 Å | ||||||
Authors | Pandelieva, A.T. / Tremblay, V. / Sarvan, S. / Chica, R.A. / Couture, J.-F. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Brighter Red Fluorescent Proteins by Rational Design of Triple-Decker Motif. Authors: Pandelieva, A.T. / Baran, M.J. / Calderini, G.F. / McCann, J.L. / Tremblay, V. / Sarvan, S. / Davey, J.A. / Couture, J.F. / Chica, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h88.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h88.ent.gz | 155.5 KB | Display | PDB format |
PDBx/mmJSON format | 5h88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h88_validation.pdf.gz | 450.6 KB | Display | wwPDB validaton report |
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Full document | 5h88_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 5h88_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 5h88_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/5h88 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/5h88 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27624.076 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: PAmCherry / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWW2*PLUS #2: Water | ChemComp-HOH / | Source details | THIS SEQUENCE WAS BASED ON THE PAMCHERRY1 PROTEIN (UNP REFERENCE D1MPT3). RESIDUES MET 64, TYR 65, ...THIS SEQUENCE WAS BASED ON THE PAMCHERRY1 PROTEIN (UNP REFERENCE D1MPT3). RESIDUES MET 64, TYR 65, AND GLY 68 form a CHROMOPHOR | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 100mM HEPES and 25% Peg3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→30.16 Å / Biso Wilson estimate: 36.76 Å2 |
-Processing
Software |
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Refinement | Resolution: 2.06→30.16 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.185 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.158
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Displacement parameters | Biso mean: 41.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→30.16 Å
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Refine LS restraints |
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