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- PDB-6l26: Neutron crystal structure of the mutant green fluorescent protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6l26 | |||||||||
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Title | Neutron crystal structure of the mutant green fluorescent protein (EGFP) | |||||||||
![]() | Green fluorescent protein | |||||||||
![]() | FLUORESCENT PROTEIN / GFP / mutant / recombinant | |||||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / trideuteriooxidanium / DEUTERATED WATER / Green fluorescent protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / ![]() | |||||||||
![]() | Adachi, M. / Shimizu, R. / Shibazaki, C. / Kagotani, Y. / Ostermann, A. / Schrader, T.E. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Direct Observation of the Protonation States in the Mutant Green Fluorescent Protein. Authors: Shibazaki, C. / Shimizu, R. / Kagotani, Y. / Ostermann, A. / Schrader, T.E. / Adachi, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128 KB | Display | ![]() |
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PDB format | ![]() | 101.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 359.1 KB | Display | ![]() |
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Full document | ![]() | 361.2 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6l27C ![]() 2wurS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25843.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The amino acids of TYG are processed to chromophore as CRO by post-translational reaction. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-D3O / |
#3: Chemical | ChemComp-DOD / |
Has ligand of interest | Y |
Sequence details | Residue SER 66 has been mutated to THR 66. Residues THR 66, TYR 67 and GLY 68 constitute the ...Residue SER 66 has been mutated to THR 66. Residues THR 66, TYR 67 and GLY 68 constitute the chromophore CRO 66. |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES-NaOD (pD 7.0), 5.0 % w/v PEG 2000 and 50 mM NDSB |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: NUCLEAR REACTOR / Site: FRM II ![]() |
Detector | Type: BIODIFF / Detector: IMAGE PLATE / Date: Nov 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 2.668 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→24.8 Å / Num. obs: 90310 / % possible obs: 88.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.45→1.49 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 25594 / % possible all: 73.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WUR Resolution: 1.444→24.764 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 0.88→39.362 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: NEUTRON DIFFRACTION / Rfactor Rfree error: 0
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