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Open data
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Basic information
Entry | Database: PDB / ID: 3zuj | |||||||||
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Title | Padron on (fluorescent) ABcis | |||||||||
![]() | FLUORESCENT PROTEIN DRONPA | |||||||||
![]() | FLUORESCENT PROTEIN / GFP VARIANTS / POSITIVE PHOTOSWITCHING / FPS / RSFPS / CRYO-PROBE / INTERMEDIATE STATE / ISOMERIZATION | |||||||||
Function / homology | ![]() bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | REGIS Faro, A. / Carpentier, P. / Bourgeois, D. | |||||||||
![]() | ![]() Title: Low-Temperature Chromophore Isomerization Reveals the Photoswitching Mechanism of the Fluorescent Protein Padron. Authors: Regis Faro, A. / Carpentier, P. / Jonasson, G. / Pompidor, G. / Arcizet, D. / Demachy, I. / Bourgeois, D. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 279.3 KB | Display | ![]() |
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PDB format | ![]() | 230.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.1 KB | Display | ![]() |
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Full document | ![]() | 488.2 KB | Display | |
Data in XML | ![]() | 54.1 KB | Display | |
Data in CIF | ![]() | 74.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3zufC ![]() 3zulC ![]() 2z1oS 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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6 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24518.703 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.45 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 500 MM MG(NO3)2, 50 MM HEPES (PH 7.5), 26% PEG 3350 AS CRYSTALLIZATION BUFFER. OPTIMIZED CRYSTALS WERE THEN OBTAINED BY MICRO-SEEDING IN THE SAME BUFFER, EXCEPT THAT A REDUCED AMOUNT OF PEG 3350 WAS USED (16%). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→50 Å / Num. obs: 61045 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.23 % / Biso Wilson estimate: 26.63 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.91 |
Reflection shell | Resolution: 2.34→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.29 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Z1O Resolution: 2.345→46.544 Å / SU ML: 0.83 / σ(F): 1.99 / Phase error: 24.34 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.431 Å2 / ksol: 0.321 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2
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Refinement step | Cycle: LAST / Resolution: 2.345→46.544 Å
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Refine LS restraints |
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LS refinement shell |
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