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Yorodumi- PDB-4zrr: Crystal Structure of Monomeric Bacteriophytochrome mutant D207L Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zrr | |||||||||||||||||||||
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Title | Crystal Structure of Monomeric Bacteriophytochrome mutant D207L Y263F at 1.5 A resolution Using a home source. | |||||||||||||||||||||
Components | Bacteriophytochrome | |||||||||||||||||||||
Keywords | TRANSFERASE / BACTERIOPHYTOCHROME / PAS / GAF / BILIVERDIN / SIGNALING PROTEIN | |||||||||||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||||||||||||||
Authors | Bhattacharya, S. / Satyshur, K.A. / Lehtivuori, H. / Forest, K.T. | |||||||||||||||||||||
Funding support | Finland, United States, 6items
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Citation | Journal: Front Mol Biosci / Year: 2015 Title: Removal of Chromophore-Proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor. Authors: Lehtivuori, H. / Bhattacharya, S. / Angenent-Mari, N.M. / Satyshur, K.A. / Forest, K.T. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zrr.cif.gz | 268.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zrr.ent.gz | 216.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zrr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/4zrr ftp://data.pdbj.org/pub/pdb/validation_reports/zr/4zrr | HTTPS FTP |
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-Related structure data
Related structure data | 4z1wC 4o8gS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37183.344 Da / Num. of mol.: 1 / Mutation: F145S,D207L, Y263F, L311E, L314E Source method: isolated from a genetically manipulated source Details: T7 Expression vector is on the N-terminal end and is present in the crystallized protein but not seen. Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: bphP, DR_A0050 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9RZA4, histidine kinase |
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-Non-polymers , 5 types, 293 molecules
#2: Chemical | ChemComp-LBV / | ||
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#3: Chemical | ChemComp-LBW / | ||
#4: Chemical | ChemComp-PO4 / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 51.62 % / Description: Green prismatic crystals. |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Crystals of D207L-Y263F phytochrome mutant were grown from hanging drop vapor diffusion in 20% PEG400, starting protein concentration of 20 mg/ml, and 0.1M phosphate citrate buffer at pH 4.0. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Feb 14, 2015 |
Radiation | Monochromator: Goebel Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.6 Å / Num. obs: 54864 / % possible obs: 96 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.84 Å2 / Rsym value: 0.05 / Net I/σ(I): 14.69 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 4.83 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4O8G Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.403 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.071 / 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: 18.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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