+Open data
-Basic information
Entry | Database: PDB / ID: 2phy | |||||||||
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Title | PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED) | |||||||||
Components | PHOTOACTIVE YELLOW PROTEIN | |||||||||
Keywords | PHOTORECEPTOR / LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS | |||||||||
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 / Resolution: 1.4 Å | |||||||||
Authors | Borgstahl, G.E.O. / Getzoff, E.D. | |||||||||
Citation | Journal: Biochemistry / Year: 1995 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. #1: Journal: Biochemistry / Year: 1994 Title: Complete Chemical Structure of Photoactive Yellow Protein: Novel Thioester-Linked 4-Hydroxycinnamyl Chromophore and Photocycle Chemistry Authors: Baca, M. / Borgstahl, G.E.O. / Boissinot, M. / Burke, P.M. / Williams, D.R. / Slater, K.A. / Getzoff, E.D. | |||||||||
History |
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Remark 650 | HELIX HELIX DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM CHECKED BY HAND ON THE GRAPHICS DISPLAY. | |||||||||
Remark 700 | SHEET SHEET SHEET_ID: B-1; DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM CHECKED BY HAND ON THE ...SHEET SHEET SHEET_ID: B-1; DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM CHECKED BY HAND ON THE GRAPHICS DISPLAY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2phy.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2phy.ent.gz | 26.8 KB | Display | PDB format |
PDBx/mmJSON format | 2phy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2phy_validation.pdf.gz | 376.3 KB | Display | wwPDB validaton report |
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Full document | 2phy_full_validation.pdf.gz | 376.4 KB | Display | |
Data in XML | 2phy_validation.xml.gz | 4.1 KB | Display | |
Data in CIF | 2phy_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/2phy ftp://data.pdbj.org/pub/pdb/validation_reports/ph/2phy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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 natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9626 / References: UniProt: P16113 |
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#2: Chemical | ChemComp-HC4 / |
#3: Water | ChemComp-HOH / |
Compound details | COMPND MOLECULE: PHOTOACTIVE YELLOW PROTEIN. 4-HYDROXYCINNAMYL CHROMOPHORE COVALENTLY LINKED TO ...COMPND MOLECULE: PHOTOACTIV |
Nonpolymer details | 4-HYDROXYCINNAMYL CHROMOPHORE, O(C6H4)CH=CH(C=O), IS COVALENTLY LINKED TO CYSTEINE 69 BY A ...4-HYDROXYCIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.17 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop / Details: used as seeds | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Date: Nov 1, 1991 |
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Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1.4 Å / Num. obs: 19756 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 |
Reflection | *PLUS Lowest resolution: 9999 Å / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.5 Å / Num. unique obs: 3449 / Num. measured obs: 4910 / Rmerge(I) obs: 0.207 |
-Processing
Software |
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Refinement | Resolution: 1.4→20 Å / σ(F): 3
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Displacement parameters | Biso mean: 13.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.5 Å / Rfactor Rfree: 0.222 / Num. reflection obs: 2030 / Rfactor obs: 0.212 |