+
Open data
-
Basic information
Entry | Database: PDB / ID: 2pyr | ||||||
---|---|---|---|---|---|---|---|
Title | PHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K) | ||||||
![]() | PHOTOACTIVE YELLOW PROTEIN | ||||||
![]() | PHOTORECEPTOR / LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS | ||||||
Function / homology | ![]() photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Perman, B. / Srajer, V. / Ren, Z. / Teng, T.Y. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. ...Perman, B. / Srajer, V. / Ren, Z. / Teng, T.Y. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. / Hellingwerf, K. / Moffat, K. | ||||||
![]() | ![]() Title: Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle. Authors: Perman, B. / Srajer, V. / Ren, Z. / Teng, T. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. / Hellingwerf, K. / Moffat, K. #1: ![]() Title: 1.4 A Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore Authors: Borgstahl, G.E. / Williams, D.R. / Getzoff, E.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 36.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 379.1 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13888.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THIOESTER LINK BETWEEN SG CYS 69 AND C1 HC4 150 / Source: (gene. exp.) ![]() Description: 4-HYDROXY CINNAMIC ANHYDRIDE CHROMOPHORE RECONSTITUTION Gene: P16113 / Plasmid: M15-PHISP / Production host: ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.17 % / Description: INITIAL PHASES ARE FROM 2PHY | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: seeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: THOMPSON / Detector: CCD AREA DETECTOR / Date: Nov 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): L / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 13027 / % possible obs: 83.4 % / Redundancy: 14 % / Rmerge(I) obs: 0.092 |
Reflection shell | Resolution: 1.5→1.57 Å / Redundancy: 14 % / % possible all: 44.8 |
Reflection shell | *PLUS % possible obs: 44.8 % |
-
Processing
Software |
| ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.9→20 Å / % reflection Rfree: 10 % / Cross valid method: FREE-R Details: TERWILLIGER/BERENDZEN DIFFERENCE REFINEMENT G RESIDUE IS DARK STRUCTURE, PG R RESIDE IS 1 NANOSECOND STRUCTURE, [PR]. ONLY DIFFERENT CONFORMATIONS AFTER 1 NANOSECOND INCLUDED. | ||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
| ||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rfree: 0.185 | ||||||||||||||
Solvent computation | *PLUS | ||||||||||||||
Displacement parameters | *PLUS |