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Open data
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Basic information
Entry | Database: PDB / ID: 3lsa | |||||||||
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Title | Padron0.9-OFF (non-fluorescent state) | |||||||||
![]() | Padron0.9 | |||||||||
![]() | FLUORESCENT PROTEIN / beta barrel / cis-trans isomerisation | |||||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / SPERMIDINE![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Brakemann, T. / Weber, G. / Trowitzsch, S. / Wahl, M.C. / Jakobs, S. | |||||||||
![]() | ![]() Title: Molecular basis of the light-driven switching of the photochromic fluorescent protein Padron. Authors: Brakemann, T. / Weber, G. / Andresen, M. / Groenhof, G. / Stiel, A.C. / Trowitzsch, S. / Eggeling, C. / Grubmuller, H. / Hell, S.W. / Wahl, M.C. / Jakobs, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.6 KB | Display | ![]() |
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PDB format | ![]() | 174.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 510.2 KB | Display | ![]() |
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Full document | ![]() | 536.3 KB | Display | |
Data in XML | ![]() | 47.4 KB | Display | |
Data in CIF | ![]() | 66 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ls3C ![]() 2iovS 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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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 26973.525 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 753 molecules ![](data/chem/img/SPD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 35% PEG 400, 5% PEG 3000, 0.1M Hepes, 10% glycerol, 0.1M spermidine, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 21, 2008 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 83955 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 23.5 Å2 / Rsym value: 0.043 |
Reflection shell | Resolution: 1.79→1.86 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 16753 / Rsym value: 0.502 / % possible all: 98.3 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IOV Resolution: 1.79→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.01 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 18.652 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.839 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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