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Yorodumi- PDB-4o0p: Crystal Structure of D. radiodurans Bacteriophytochrome Photosens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o0p | ||||||
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Title | Crystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its Dark Form | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | TRANSFERASE / Phytochrome / Red-Light Photoreceptor / Photoconversion / Chromophore / Sensory Transduction / Signaling Protein / Biliverdin | ||||||
Function / homology | Function and homology information osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Takala, H. / Ihalainen, J.A. / Westenhoff, S. | ||||||
Citation | Journal: Nature / Year: 2014 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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Remark 700 | SHEET Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o0p.cif.gz | 201.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o0p.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 4o0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/4o0p ftp://data.pdbj.org/pub/pdb/validation_reports/o0/4o0p | HTTPS FTP |
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-Related structure data
Related structure data | 4o01C 2o9cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 4 - 503 / Label seq-ID: 18 - 517
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-Components
#1: Protein | Mass: 56581.027 Da / Num. of mol.: 2 / Fragment: Photosensory Core Module, UNP residues 1-502 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Gene: bphP / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9RZA4, histidine kinase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.74 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 1500, in dark, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98044 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.98044 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.8→48.65 Å / Num. all: 18561 / Num. obs: 18551 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.97 % / Biso Wilson estimate: 130.975 Å2 / Rmerge(I) obs: 0.392 / Rsym value: 0.411 / Net I/σ(I): 4.72 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O9C Resolution: 3.8→48.65 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.3487 / WRfactor Rwork: 0.3096 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7726 / SU B: 32.817 / SU ML: 0.502 / SU Rfree: 0.1421 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.142 / 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: 355.56 Å2 / Biso mean: 210.2428 Å2 / Biso min: 67.51 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→48.65 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 7295 / Type: TIGHT THERMAL / Rms dev position: 24.25 Å / Weight position: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.8→3.898 Å / Total num. of bins used: 20
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