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- PDB-1s4s: Reaction Intermediate in the Photocycle of PYP, intermediate occu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s4s | ||||||
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Title | Reaction Intermediate in the Photocycle of PYP, intermediate occupied between 100 micro-seconds to 5 milli-seconds | ||||||
![]() | Photoactive yellow protein | ||||||
![]() | PHOTOSYNTHESIS / reaction intermediate | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmidt, M. / Pahl, R. / Srajer, V. / Anderson, S. / Ren, Z. / Ihee, H. / Rajagopal, S. / Moffat, K. | ||||||
![]() | ![]() Title: Protein kinetics: Structures of intermediates and reaction mechanism from time-resolved x-ray data Authors: Schmidt, M. / Pahl, R. / Srajer, V. / Anderson, S. / Ren, Z. / Ihee, H. / Rajagopal, S. / Moffat, K. #1: ![]() Title: Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data Authors: Schmidt, M. / Rajagopal, S. / Ren, Z. / Moffat, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.2 KB | Display | ![]() |
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PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.9 KB | Display | ![]() |
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Full document | ![]() | 379.1 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1s4rC ![]() 2phyS 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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Unit cell |
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Components
#1: Protein | Mass: 13888.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammoniumsulphate, Potassium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction |
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Radiation |
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Reflection | Resolution: 1.9→40 Å / Num. all: 8326 / Num. obs: 8326 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2phy Resolution: 1.9→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residue 69 consits of Cys69 and the attached chromophore hydroxy-cinnamic acid. Dihedral of atoms O1 (carbonyl oxygen of chromophore), C1, C2 and C3 was inititally restrained to 0 deg (cis ...Details: Residue 69 consits of Cys69 and the attached chromophore hydroxy-cinnamic acid. Dihedral of atoms O1 (carbonyl oxygen of chromophore), C1, C2 and C3 was inititally restrained to 0 deg (cis planar). The restraint was reset to zero in the last cycle, the angle refined to 22 deg.
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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