+Open data
-Basic information
Entry | Database: PDB / ID: 3ls3 | |||||||||
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Title | Padron0.9-ON (fluorescent state) | |||||||||
Components | Padron0.9 | |||||||||
Keywords | FLUORESCENT PROTEIN / beta-barrel / cis-trans isomerisation | |||||||||
Function / homology | Green Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / SPERMIDINE Function and homology information | |||||||||
Biological species | Pectiniidae (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | |||||||||
Authors | Brakemann, T. / Weber, G. / Trowitzsch, S. / Wahl, M.C. / Jakobs, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ls3.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ls3.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ls3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/3ls3 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3ls3 | HTTPS FTP |
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-Related structure data
Related structure data | 3lsaC 2iovS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26973.525 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectiniidae (invertebrata) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SPD / #4: Chemical | ChemComp-EPE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.09 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X10SA |
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 | Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 109915 / Num. obs: 110246 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.036 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 10889 / Rsym value: 0.618 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IOV Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.649 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / 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: 20.686 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.695 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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