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Yorodumi- PDB-4y5f: PAS-GAF fragment from Deinococcus radiodurans BphP assembled with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y5f | ||||||||||||||||||
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Title | PAS-GAF fragment from Deinococcus radiodurans BphP assembled with BV - Y307S, high dose | ||||||||||||||||||
Components | Bacteriophytochrome | ||||||||||||||||||
Keywords | TRANSFERASE / high-dose / spectroscopy / bilin chromophore / phythochrome | ||||||||||||||||||
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: 1.7 Å | ||||||||||||||||||
Authors | Li, F. / Burgie, E.S. / Yu, T. / Heroux, A. / Schatz, G.C. / Vierstra, R.D. / Orville, A.M. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome. Authors: Li, F. / Burgie, E.S. / Yu, T. / Heroux, A. / Schatz, G.C. / Vierstra, R.D. / Orville, A.M. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y5f.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y5f.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 4y5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/4y5f ftp://data.pdbj.org/pub/pdb/validation_reports/y5/4y5f | HTTPS FTP |
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-Related structure data
Related structure data | 4y3iC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34463.324 Da / Num. of mol.: 1 / Fragment: PAS-GAF fragment (UNP residues 4-321) / Mutation: Y307S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Gene: bphP, DR_A0050 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase |
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#2: Chemical | ChemComp-LBV / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 10% PEG3350, 19% isopropanol, 5% glycerol, 100 mM citric acid/NaOH, ph 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 33245 / % possible obs: 96.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.8 / % possible all: 76.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2O9C Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.155 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.207 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→50 Å
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Refine LS restraints |
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