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- PDB-4o01: Crystal Structure of D. radiodurans Bacteriophytochrome Photosens... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4o01 | ||||||
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Title | Crystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its Illuminated Form | ||||||
![]() | Bacteriophytochrome | ||||||
![]() | TRANSFERASE / Phytochrome / Red-Light Photoreceptor / Photoconversion / Chromophore / Sensory Transduction / Signaling Protein / Biliverdin | ||||||
Function / homology | ![]() osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takala, H. / Ihalainen, J.A. / Westenhoff, S. | ||||||
![]() | ![]() Title: Signal amplification and transduction in phytochrome photosensors Authors: Takala, H. / Bjorling, A. / Berntsson, O. / Lehtivuori, H. / Niebling, S. / Hoernke, M. / Kosheleva, I. / Henning, R. / Menzel, A. / Ihalainen, J.A. / Westenhoff, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 378.8 KB | Display | ![]() |
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PDB format | ![]() | 311.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 70.1 KB | Display | |
Data in CIF | ![]() | 90.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4o0pC ![]() 2o9cS C: citing same article ( 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 6 - 506 / Label seq-ID: 20 - 520
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 56581.027 Da / Num. of mol.: 4 / Fragment: Photosensory Core Module, UNP residues 1-502 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: R1 / Gene: bphP / Plasmid: pET21b(+) / Production host: ![]() ![]() #2: Chemical | ChemComp-LBV / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, 0.2M NaCl, 25% PEG 3350, sequential 655nm illumination, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98043 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.24→49.22 Å / Num. all: 61961 / Num. obs: 61928 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.31 % / Biso Wilson estimate: 118.652 Å2 / Rmerge(I) obs: 0.241 / Rsym value: 0.248 / Net I/σ(I): 9.69 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2O9C Resolution: 3.24→49.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 26.072 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 279.15 Å2 / Biso mean: 158.6115 Å2 / Biso min: 80.57 Å2
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Refinement step | Cycle: LAST / Resolution: 3.24→49.22 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5
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LS refinement shell | Resolution: 3.24→3.324 Å / Total num. of bins used: 20
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