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Yorodumi- PDB-3t50: X-ray structure of the LOV domain from the LOV-HK sensory protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t50 | ||||||
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Title | X-ray structure of the LOV domain from the LOV-HK sensory protein from Brucella abortus (dark state). | ||||||
Components | Blue-light-activated histidine kinase | ||||||
Keywords | TRANSFERASE / PAS superfamily / Blue-light photoreceptor / FMN binding | ||||||
Function / homology | Function and homology information protein histidine kinase activity / response to stimulus / histidine kinase / photoreceptor activity / ATP binding Similarity search - Function | ||||||
Biological species | Brucella melitensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Rinaldi, J.J. / Klinke, S. / Goldbaum, F.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: The Beta-Scaffold of the LOV Domain of the Brucella Light-Activated Histidine Kinase Is a Key Element for Signal Transduction Authors: Rinaldi, J. / Gallo, M. / Klinke, S. / Paris, G. / Bonomi, H.R. / Bogomolni, R.A. / Cicero, D.O. / Goldbaum, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t50.cif.gz | 62.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t50.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 3t50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t50 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t50 | HTTPS FTP |
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-Related structure data
Related structure data | 2v0wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14420.438 Da / Num. of mol.: 2 / Fragment: LOV domain, residues 28-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: Brucella melitensis biovar Abortus 2308 / Gene: BAB2_0652, BMEII0679 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YC53, 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 Å3/Da / Density % sol: 38.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 2000 MME, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 16, 2010 / Details: Varimax-HF confocal multilayer mirrors |
Radiation | Monochromator: Varimax-HF, confocal multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→20 Å / Num. all: 28947 / Num. obs: 28520 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.64→1.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1961 / Rsym value: 0.285 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2V0W Resolution: 1.64→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.8 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.68 Å
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