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Yorodumi- PDB-1uwn: The Initial Events in the Photocycle of Photoactive Yellow Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uwn | ||||||
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Title | The Initial Events in the Photocycle of Photoactive Yellow Protein: A Common Mechanism on Light Activation in Photoreceptor Proteins | ||||||
Components | PHOTOACTIVE YELLOW PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / PAS / LOV / PHOTOCYCLE / PHOTORECEPTOR | ||||||
Function / homology | Function and homology information photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | HALORHODOSPIRA HALOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å | ||||||
Authors | Kort, R. / Hellingwerf, K.J. / Ravelli, R.B.G. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2004 Title: Initial events in the photocycle of photoactive yellow protein. Authors: Kort, R. / Hellingwerf, K.J. / Ravelli, R.B. #1: Journal: Photochem.Photobiol. / Year: 2003 Title: Characterization of Photocycle Intermediates in Crystalline Photoactive Yellow Protein Authors: Kort, R. / Ravelli, R.B.G. / Schotte, F. / Bourgeois, D. / Crielaard, W. / Hellingwerf, K.J. / Wulff, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uwn.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uwn.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 1uwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/1uwn ftp://data.pdbj.org/pub/pdb/validation_reports/uw/1uwn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14123.052 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DARK STATE, GROUND STATE (PG) / Source: (gene. exp.) HALORHODOSPIRA HALOPHILA (bacteria) / Strain: BN9626 Description: HALORHODOSPIRA HALOPHILA WAS PREVIOUSLY KNOWN AS ECTOTHIORHODOSPIRA HALOPHILA Cell: BACTERIUM / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/ PREP4 PHISP / References: UniProt: P16113 | ||||
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#2: Chemical | ChemComp-HC4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE MET-RESIDUES WERE SUBSTITUTE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 20 % Description: STATISTICS ARE GIVEN FOR REMOTE DATA SET (2 SWEEPS) |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K |
-Data collection
Diffraction | Mean temperature: 85 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393, 0.9796 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 30, 2002 / Details: BENT MIRROR | |||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.2→30 Å / Num. obs: 159748 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.9 | |||||||||
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 5.5 / % possible all: 92.4 | |||||||||
Reflection | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 30 Å / Num. obs: 60337 / % possible obs: 97.1 % / Num. measured all: 159748 / Rmerge(I) obs: 0.033 | |||||||||
Reflection shell | *PLUS % possible obs: 91.1 % / Num. unique obs: 4034 / Num. measured obs: 7373 / Rmerge(I) obs: 0.171 / Mean I/σ(I) obs: 4.2 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 1.2→40 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.466 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE EXPERIMENTAL DENSITY SHOWS MAIN-CHAIN DISORDER FOR RESIDUES 16-18 AND 115-117. THE FIRST 3 RESIDUES (MSE1-HIS3) ARE DISORDERED AS WELL.
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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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→40 Å
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