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Open data
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Basic information
Entry | Database: PDB / ID: 6l02 | ||||||
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Title | Crystal Structure of sfYFP66BPAC203Y | ||||||
![]() | Yellow fluorescent protein | ||||||
![]() | FLUORESCENT PROTEIN | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Yellow fluorescent protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zheng, D. / Yu, L.-J. / Liu, X. / Wang, J. | ||||||
![]() | ![]() Title: Ultrafast Photoinduced Electron Transfer in a Photosensitizer Protein Authors: Zheng, D. / Tao, M. / Yu, L.J. / Liu, X. / Xia, A. / Wang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.6 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.7 KB | Display | ![]() |
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Full document | ![]() | 429.7 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yr3S S: Starting model for refinement |
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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: 26997.514 Da / Num. of mol.: 1 Mutation: S30R,N39I,C48S,V68L,E95C,T105K,E111V,I128T,H148E,K166T,I167V,S205T,A206V,H231L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
Sequence details | RESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6 / Details: PEG 3350, sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.799→20 Å / Num. obs: 23452 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.02683 / Rpim(I) all: 0.02683 / Rrim(I) all: 0.03795 / Net I/σ(I): 21.84 |
Reflection shell | Resolution: 1.799→1.863 Å / Rmerge(I) obs: 0.1802 / Num. unique obs: 2297 / CC1/2: 0.903 / Rpim(I) all: 0.1802 / Rrim(I) all: 0.2548 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5YR3 Resolution: 1.799→19.518 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.94 Å2 / Biso mean: 36.8979 Å2 / Biso min: 19.76 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.799→19.518 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -0.2019 Å / Origin y: 7.9467 Å / Origin z: 22.8394 Å
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Refinement TLS group | Selection details: all |