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- PDB-6r26: The photosensory core module (PAS-GAF-PHY) of the bacterial phyto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r26 | |||||||||||||||||||||
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Title | The photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state | |||||||||||||||||||||
![]() | Bacteriophytochrome protein | |||||||||||||||||||||
![]() | SIGNALING PROTEIN / photoreceptor / bilin protein / locked chromophore / crystallographic superstructure | |||||||||||||||||||||
Function / homology | ![]() red or far-red light photoreceptor activity / red, far-red light phototransduction / osmosensory signaling via phosphorelay pathway / protein histidine kinase activity / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Scheerer, P. / Michael, N. / Lamparter, T. / Krauss, N. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of the photosensory core module of bacteriophytochrome Agp1 reveal pronounced structural flexibility of this protein in the red-absorbing Pr state Authors: Scheerer, P. / Schmidt, A. / Nagano, S. / Qureshi, B. / Szczepek, M. / Sauthof, L. / Michael, N. / Inomata, K. / Lamparter, T. / Krauss, N. #1: Journal: J. Struct. Biol. / Year: 2006 Title: Crystallization and preliminary X-ray crystallographic analysis of the N-terminal photosensory module of phytochrome Agp1, a biliverdin-binding photoreceptor from Agrobacterium tumefaciens. Authors: Scheerer, P. / Michael, N. / Park, J.H. / Noack, S. / Foerster, C. / Hammam, M.A. / Inomata, K. / Choe, H.W. / Lamparter, T. / Krauss, N. #2: ![]() Title: The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers. Authors: Nagano, S. / Scheerer, P. / Zubow, K. / Michael, N. / Inomata, K. / Lamparter, T. / Krauss, N. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.4 KB | Display | ![]() |
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PDB format | ![]() | 159 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 768.2 KB | Display | ![]() |
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Full document | ![]() | 773.6 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r27C ![]() 5i5lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56463.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: C58 / ATCC 33970 / Gene: Atu1990 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-JQ2 / |
#3: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 20-23% PEG 3350, 50 mM NaCl and 100 mM Tris/Cl, in 30% PEG 3350 as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 |
Reflection | Resolution: 3.11→46.84 Å / Num. obs: 11232 / % possible obs: 99.3 % / Redundancy: 9.4 % / Biso Wilson estimate: 95.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.041 / Rrim(I) all: 0.093 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 3.11→3.32 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 5 / Num. unique obs: 1987 / CC1/2: 0.962 / Rpim(I) all: 0.175 / Rrim(I) all: 0.397 / Χ2: 0.62 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5I5L Resolution: 3.11→46.84 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 47.757 / SU ML: 0.403 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.842 Å2
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Refinement step | Cycle: LAST / Resolution: 3.11→46.84 Å
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Refine LS restraints |
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