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Open data
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Basic information
Entry | Database: PDB / ID: 5yr3 | ||||||
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Title | Structure of sfYFP66BPA | ||||||
![]() | Yellow fluorescent protein | ||||||
![]() | FLUORESCENT PROTEIN / Bioluminescence Protein Chromophore Linkage | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kang, F. / Wang, L. / Wang, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: sfYFP66BPA Authors: Kang, F. / Wang, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.9 KB | Display | ![]() |
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PDB format | ![]() | 84.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.7 KB | Display | ![]() |
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Full document | ![]() | 440.5 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qyoS 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: 25434.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
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: 2.31 Å3/Da / Density % sol: 46.77 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 15% PEG 3350, 0.1M malic acid, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.434 Å / Num. obs: 19926 / % possible obs: 99.2 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.9→2.02 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.89 / Num. unique obs: 3150 / CC1/2: 0.93 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1qyo Resolution: 1.901→29.432 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→29.432 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.4003 Å / Origin y: 7.8323 Å / Origin z: 22.8252 Å
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Refinement TLS group | Selection details: all |