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Yorodumi- PDB-6qq9: Cryogenic temperature structure of the fluorescent protein Cerule... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qq9 | ||||||
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Title | Cryogenic temperature structure of the fluorescent protein Cerulean recorded after an accumulated dose of 5.8 MGy | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / tryptophan-based chromophore / Cerulean / hydrogen atoms | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 Å | ||||||
Authors | Gotthard, G. / Aumonier, S. / Royant, A. | ||||||
Citation | Journal: Iucrj / Year: 2019 Title: Specific radiation damage is a lesser concern at room temperature. Authors: Gotthard, G. / Aumonier, S. / De Sanctis, D. / Leonard, G. / von Stetten, D. / Royant, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qq9.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qq9.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qq9_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 6qq9_full_validation.pdf.gz | 432.5 KB | Display | |
Data in XML | 6qq9_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 6qq9_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/6qq9 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/6qq9 | HTTPS FTP |
-Related structure data
Related structure data | 6qq8C 6qqaC 6qqbC 6qqcC 6qqdC 6qqeC 6qqfC 6qqhC 6qqiC 6qqjC 6qqkC 6qsaC C: citing same article (ref.) |
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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: 26789.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#2: Chemical | ChemComp-CO2 / |
#3: 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: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100mM HEPES 7.0, 12% PEG8000, 100mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2014 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→46.99 Å / Num. obs: 21133 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.708 Å2 / CC1/2: 1 / Net I/σ(I): 28.23 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1544 / CC1/2: 0.726 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.82→46.99 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.202 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / 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: 33.889 Å2
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Refinement step | Cycle: 1 / Resolution: 1.82→46.99 Å
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Refine LS restraints |
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