+Open data
-Basic information
Entry | Database: PDB / ID: 4ijg | ||||||
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Title | Crystal structure of monomeric bacteriophytochrome | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | SIGNALING PROTEIN / bacteriophytochrome / PAS / GAF / 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 / molecular replacement / Resolution: 1.701 Å | ||||||
Authors | Auldridge, M.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Origins of fluorescence in evolved bacteriophytochromes. Authors: Bhattacharya, S. / Auldridge, M.E. / Lehtivuori, H. / Ihalainen, J.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 | 4ijg.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ijg.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ijg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ijg ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ijg | HTTPS FTP |
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-Related structure data
Related structure data | 4o8gC 3s7qS 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: 36991.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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(DE3) / References: UniProt: Q9RZA4, histidine kinase |
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-Non-polymers , 5 types, 216 molecules
#2: Chemical | ChemComp-LBV / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 25% PEG 400, 2.5 %glycerol, 0.1M phosphate citrate, pH 4.2, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 29, 2011 / Details: monochromator | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→25 Å / Num. obs: 37460 / % possible obs: 94.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.062 / Net I/σ(I): 15.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3S7Q Resolution: 1.701→23.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2551 / WRfactor Rwork: 0.2299 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8422 / SU B: 2.077 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1187 / SU Rfree: 0.1098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.88 Å2 / Biso mean: 25.5719 Å2 / Biso min: 12.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.119 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.701→23.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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