[English] 日本語
![](img/lk-miru.gif)
- PDB-6r27: Crystallographic superstructure of the photosensory core module (... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6r27 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystallographic superstructure of 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 | ![]()
| |||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 713.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 605.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 66.9 KB | Display | |
Data in CIF | ![]() | 87.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r26C ![]() 5hsqS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
|
-
Components
#1: Protein | Mass: 56463.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: C58 / ATCC 33970 / Gene: Atu1990 / Production host: ![]() ![]() #2: Chemical | ChemComp-JQ2 / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % / Description: tetragonal prism |
---|---|
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 20% Sucrose as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→47.89 Å / Num. obs: 32444 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 68.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.079 / Rrim(I) all: 0.128 / Χ2: 0.95 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4659 / CC1/2: 0.87 / Rpim(I) all: 0.341 / Rrim(I) all: 0.557 / Χ2: 0.94 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5HSQ Resolution: 3.4→47.89 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.859 / SU B: 86.901 / SU ML: 0.613 / Cross valid method: THROUGHOUT / ESU R Free: 0.717 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.097 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→47.89 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|