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Yorodumi- PDB-2o9b: Crystal Structure of Bacteriophytochrome chromophore binding domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o9b | ||||||
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Title | Crystal Structure of Bacteriophytochrome chromophore binding domain | ||||||
Components | Bacteriophytochrome | ||||||
Keywords | TRANSFERASE / phytochrome chromophore / figure-of-eight knot / phytochromobilin / biliverdin / PAS / GAF | ||||||
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: 2.15 Å | ||||||
Authors | Wagner, J.R. / Brunzelle, J.S. / Vierstra, R.D. / Forest, K.T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: High resolution structure of deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. Authors: Wagner, J.R. / Zhang, J. / Brunzelle, J.S. / Vierstra, R.D. / 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 | 2o9b.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o9b.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 2o9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/2o9b ftp://data.pdbj.org/pub/pdb/validation_reports/o9/2o9b | HTTPS FTP |
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-Related structure data
Related structure data | 2o9cC 1ztuS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37024.250 Da / Num. of mol.: 1 / Fragment: chromophore binidng domain / Mutation: Y307S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: bphP / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.095 M sodium citrate, 19% v/v isopropanol, 19% v/v PEG 4000, 5% V/V glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 |
Detector | Type: BRUKER PROTEUM / Detector: CCD / Date: Oct 27, 2005 / Details: Bruker Montel mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→24 Å / Num. all: 18137 / Num. obs: 17484 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.7 / % possible all: 78.8 |
-Phasing
Phasing MR | Rfactor: 0.44 / Cor.coef. Fo:Fc: 0.637 / Cor.coef. Io to Ic: 0.632
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ZTU without chromophore or his tag Resolution: 2.15→23.71 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.609 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.353 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→23.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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