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Open data
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Basic information
Entry | Database: PDB / ID: 1uwp | ||||||
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Title | Initial Events in the Photocycle of Photoactive Yellow Protein | ||||||
![]() | PHOTOACTIVE YELLOW PROTEIN | ||||||
![]() | SIGNALING PROTEIN / PAS / LOV / GAF / DOMAINS / FOLD PHOTOCYCLE / PHOTOACTIVE / PHOTORECEPTOR / YELLOW | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kort, R. / Hellingwerf, K.J. / Ravelli, R.B.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.6 KB | Display | ![]() |
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PDB format | ![]() | 59.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387 KB | Display | ![]() |
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Full document | ![]() | 389.3 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 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: LIGHT STATE / Source: (gene. exp.) ![]() Description: HALORHODOSPIRA HALOPHILA PREVIOUSLY KNOWN AS ECTOTHIORHODOSPIRA HALOPHILA Plasmid: PQE30 / Production host: ![]() ![]() | ||||
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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: ![]() |
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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: ![]() ![]() ![]() | |||||||||
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: 146753 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 14.6 | |||||||||
Reflection shell | Resolution: 1.2→1.23 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.5 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN EARLY INTERMEDIATE OF THE PHOTOCYCLE OF PYP WAS DETERMINED BY THE DATA COLLECTION OF 2 MAD DATA SETS ON ONE CRYSTAL OF PYP. THE FIRST ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN EARLY INTERMEDIATE OF THE PHOTOCYCLE OF PYP WAS DETERMINED BY THE DATA COLLECTION OF 2 MAD DATA SETS ON ONE CRYSTAL OF PYP. THE FIRST MAD DATA SET WAS OBTAINED IN THE DARK, WHEREAS THE CRYSTAL WAS ILLUMINATED FOR THE SECOND DATA SET. DATA WERE CORRECTED FOR MINOR RADIATION DAMAGE USING 2 OTHER MAD DATA SETS, COLLECTED ON AN ISOMORPHOUS CRYSTAL THAT WAS KEPT IN THE DARK. THE SAME CRYSTAL WAS USED FOR PDB- ID 1UWN.
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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: 10.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→40 Å
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Refine LS restraints |
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