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- PDB-5akp: 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: 5akp | ||||||
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Title | Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris bound to BV chromophore | ||||||
![]() | PHYTOCHROME-LIKE PROTEIN | ||||||
![]() | SIGNALING PROTEIN / PHOTORECEPTOR / BACTERIAL PROTEIN / PHOTOSENSOR / RED/FAR-RED LIGHT / PHYTOCHROME / PROTEIN STRUCTURE / SIGNAL TRANSDUCTION / XANTHOMONAS / PHYTOPATHOGEN | ||||||
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: Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas Campestris Provides Clues to its Long-Range Signaling Mechanism. Authors: Otero, L.H. / Klinke, S. / Rinaldi, J. / Velazquez-Escobar, F. / Mroginski, M.A. / Lopez, M.F. / Malamud, F. / Vojnov, A.A. / Hildebrandt, P. / Goldbaum, F.A. / 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 | ![]() | 488.9 KB | Display | ![]() |
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PDB format | ![]() | 410.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1019.3 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 45.5 KB | Display | |
Data in CIF | ![]() | 60.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gw9S S: Starting model for refinement |
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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: 71266.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THIOETHER BOND BETWEEN THE A-RING CBC SIDE CHAIN FROM BV AND THE CYS 13 Source: (gene. exp.) ![]() Strain: 8004 / Plasmid: PET-24A / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | pH: 8.3 Details: 12%(W/V) PEG 4000, 0.1 M TRIS, 0.2 M SODIUM ACETATE PH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2013 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→47.35 Å / Num. obs: 30865 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 94.46 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4GW9 Resolution: 3.25→41.75 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9049 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.453 Details: 11 N-TERMINAL RESIDUES AND RESIDUES FROM 456 TO 470 NOT MODELED, WEAK ELECTRON DENSITY IS SHOWN AT THE AREA WHERE THE D-RING FROM BV CHROMOPHORE IS PLACED.
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Displacement parameters | Biso mean: 114.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.846 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→41.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.25→3.36 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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