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Yorodumi- PDB-6kkz: Crystal structure of the S65T/F99S/M153T/V163A variant of perdeut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kkz | |||||||||
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Title | Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 8.5 | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | FLUORESCENT PROTEIN / green fluorescent protein / visualization of hydrogen / perdeuteration / high resolution | |||||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / DEUTERATED WATER / Green fluorescent protein Function and homology information | |||||||||
Biological species | Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å | |||||||||
Authors | Tai, Y. / Takaba, K. / Hanazono, Y. / Dao, H.A. / Miki, K. / Takeda, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2019 Title: X-ray crystallographic studies on the hydrogen isotope effects of green fluorescent protein at sub-angstrom resolutions Authors: Tai, Y. / Takaba, K. / Hanazono, Y. / Dao, H.A. / Miki, K. / Takeda, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kkz.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kkz.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 6kkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/6kkz ftp://data.pdbj.org/pub/pdb/validation_reports/kk/6kkz | HTTPS FTP |
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-Related structure data
Related structure data | 6kl0C 6kl1C 2wurS 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: 25857.982 Da / Num. of mol.: 1 / Mutation: S65T, F99S, M153T, V163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212 |
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#2: Chemical | ChemComp-DOD / |
Has ligand of interest | Y |
Sequence details | (1) Residue SER 65 has been mutated to THR 65. Residues THR 65, TYR 66 and GLY 67 constitute the ...(1) Residue SER 65 has been mutated to THR 65. Residues THR 65, TYR 66 and GLY 67 constitute the chromophore CRO 66. The authors state that there are some difference in the structures between CRO in database and CRO in this model. They are in the terminal carboxylic and amino groups and the protonation of phenolic oxygen. (2) Q80R was caused by a PCR error in the early study (Chalfie, M. et al., Science, 1994). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.45 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion / pH: 8.1 / Details: PEG 4000, MgCl2, Tris-DCl buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 0.9→50 Å / Num. obs: 159331 / % possible obs: 98.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 6.02 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18 |
Reflection shell | Resolution: 0.9→0.92 Å / Redundancy: 3 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 1 / Num. unique obs: 6457 / CC1/2: 0.473 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WUR Resolution: 0.9→46.137 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.26 Å2 / Biso mean: 9.1327 Å2 / Biso min: 3.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.9→46.137 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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