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- PDB-4z1w: CRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME mutant D207L Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4z1w | ||||||||||||
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Title | CRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME mutant D207L Y263F From Synchrotron | ||||||||||||
![]() | Bacteriophytochrome | ||||||||||||
![]() | TRANSFERASE / BACTERIOPHYTOCHROME / PAS / GAF / BILIVERDIN / SIGNALING PROTEIN | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Bhattacharya, S. / Satyshur, K.A. / Wangkanont, K. / Lehtivuori, H. / Forest, K.T. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.4 KB | Display | ![]() |
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PDB format | ![]() | 216.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zrrC ![]() 3s7qS ![]() 4o8gS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 37183.344 Da / Num. of mol.: 1 / Mutation: F145S,D207L Y263F, L311E, L314E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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: ![]() ![]() |
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#2: Chemical | ChemComp-LBV / |
#3: Chemical | ChemComp-LBW / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 46.76 % / Description: Green prismatic crystals. |
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Crystal grow | Temperature: 293 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. PH range: 4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→23.8 Å / Num. obs: 77741 / % possible obs: 96.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 8.8 Å2 / Rsym value: 0.052 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3S7Q, 4O8G Resolution: 1.3→23.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.146 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.042 / 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: 16.698 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→23.22 Å
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Refine LS restraints |
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