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- PDB-5uyr: Crystal structure of the dark-adapted full-length bacteriophytoch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uyr | ||||||
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Title | Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant D199A from Xanthomonas campestris | ||||||
![]() | Bacteriophytochrome | ||||||
![]() | SIGNALING PROTEIN / biliverdin / phytochrome / red-light photoreceptor / signal transduction | ||||||
Function / homology | ![]() detection of visible light / photoreceptor activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otero, L.H. / Klinke, S. / Goldbaum, F.A. / Bonomi, H.R. | ||||||
![]() | ![]() Title: Pr-favoured variants of the bacteriophytochrome from the plant pathogen Xanthomonas campestris hint on light regulation of virulence-associated mechanisms. Authors: Conforte, V. / Otero, L.H. / Toum, L. / Sirigu, S. / Antelo, G.T. / Rinaldi, J. / Foscaldi, S. / Klinke, S. / Chavas, L.M.G. / Vojnov, A.A. / Goldbaum, F.A. / Malamud, F. / Bonomi, H.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.3 KB | Display | ![]() |
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PDB format | ![]() | 195.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 44.9 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ndoC ![]() 6ndpC ![]() 5akpS 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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Unit cell |
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Components
#1: Protein | Mass: 71222.156 Da / Num. of mol.: 2 / Mutation: D199A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 8004 / Gene: bphP, XC_4241 / Plasmid: pET-24a / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 7%(W/V) PEG 4000 0.2 M SODIUM ACETATE 0.1 M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016 Details: Convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors |
Radiation | Monochromator: Cryogenically cooled channel cut Si[111] crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→48.94 Å / Num. obs: 25772 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Biso Wilson estimate: 124.23 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.048 / Rsym value: 0.172 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3.45→3.69 Å / Redundancy: 12 % / Rmerge(I) obs: 1.536 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4569 / CC1/2: 0.69 / Rpim(I) all: 0.459 / Rsym value: 1.605 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5AKP Resolution: 3.45→47.27 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.516 Details: Due to the low resolution, the initial refinement was done under LSSR restraints using the atomic coordinates from PDB:5AKP. The B-factors were refined as groups.
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Displacement parameters | Biso mean: 134.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.45→47.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.45→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
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