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Yorodumi- PDB-3ibr: Crystal Structure of P. aeruginosa Bacteriophytochrome Photosenso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ibr | ||||||
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Title | Crystal Structure of P. aeruginosa Bacteriophytochrome Photosensory Core Module Mutant Q188L in the Mixed Pr/Pfr State | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | TRANSFERASE / phytochrome / red-light photoreceptor / photoconversion / chromophore / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Photoreceptor protein / Receptor / Sensory transduction | ||||||
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 / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 Å | ||||||
Authors | Yang, X. / Kuk, J. / Moffat, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome. Authors: Yang, X. / Kuk, J. / Moffat, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ibr.cif.gz | 386.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ibr.ent.gz | 335.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ibr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/3ibr ftp://data.pdbj.org/pub/pdb/validation_reports/ib/3ibr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57371.004 Da / Num. of mol.: 2 / Fragment: UNP residues 1-497 / Mutation: Q188L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: bphP, PA4117 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21/DE3 / References: UniProt: Q9HWR3, histidine kinase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: protein: 10mg/ml, 0.5% PEG4000 (w/v), 0.01M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2007 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→50 Å / Num. all: 24681 / Num. obs: 23250 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.97→3.04 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.3 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.97→37.74 Å / SU ML: 0.52 / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.07 Å2 / ksol: 0.29 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.97→37.74 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: CHAIN B |