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Open data
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Basic information
Entry | Database: PDB / ID: 3gj1 | ||||||
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Title | Non photoactivated state of PA-GFP | ||||||
![]() | Green fluorescent protein![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Henderson, J.N. / Gepshtein, R. / Heenan, J.R. / Kallio, K. / Huppert, D. / Remington, S.J. | ||||||
![]() | ![]() Title: Structure and mechanism of the photoactivatable green fluorescent protein. Authors: Henderson, J.N. / Gepshtein, R. / Heenan, J.R. / Kallio, K. / Huppert, D. / Remington, S.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 | ![]() | 204.1 KB | Display | ![]() |
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PDB format | ![]() | 161.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3gj2C ![]() 1emaS C: citing same article ( 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: 25975.154 Da / Num. of mol.: 4 / Mutation: Q80R, F99S, M153T, V163A, T203H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ChemComp-CL / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.7 M Ammonium sulfate, 0.1 M Tris-HCl, 0.2 M Lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2008 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→50 Å / Num. obs: 91885 / % possible obs: 93.5 % / Observed criterion σ(I): 5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.044 / Χ2: 0.958 / Net I/σ(I): 25.476 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.473 / Num. unique all: 8337 / Χ2: 0.766 / % possible all: 85.8 |
-Phasing
Phasing![]() | Method: ![]() | ||||||
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Phasing MR | Rfactor: 0.549 / Cor.coef. Fo:Fc: 0.283
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1EMA Resolution: 1.8→46.37 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.81 / SU B: 3.168 / SU ML: 0.099 / SU R Cruickshank DPI: 0.146 / SU Rfree: 0.142 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.146 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.84 Å2 / Biso mean: 22.938 Å2 / Biso min: 6.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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