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Open data
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Basic information
Entry | Database: PDB / ID: 5nby | ||||||
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Title | Structure of a bacterial light-regulated adenylyl cylcase | ||||||
![]() | Beta subunit of photoactivated adenylyl cyclase | ||||||
![]() | LYASE / BLUF / adenylyl cyclase / photoreceptor / optogenetics | ||||||
Function / homology | ![]() cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Photoactivation Mechanism of a Bacterial Light-Regulated Adenylyl Cyclase. Authors: Lindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.3 KB | Display | ![]() |
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PDB format | ![]() | 119.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 723 KB | Display | ![]() |
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Full document | ![]() | 726.8 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m27SC ![]() 5m2aC ![]() 5mbbC ![]() 5mbcC ![]() 5mbdC ![]() 5mbeC ![]() 5mbgC ![]() 5mbhC ![]() 5mbjC ![]() 5mbkC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 40110.441 Da / Num. of mol.: 1 / Fragment: Beggiatoa photoactivatable adenylyl cyclase bPAC / Mutation: Y7F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M Na-HEPES pH 7.0, 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→45.501 Å / Num. obs: 13360 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 10.106 % / Biso Wilson estimate: 59.78 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.159 / Χ2: 0.963 / Net I/σ(I): 13.65 / Num. measured all: 135017 / Scaling rejects: 548 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5M27 Resolution: 2.5→45.501 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.75 Å2 / Biso mean: 74.7747 Å2 / Biso min: 38.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→45.501 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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