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Yorodumi- PDB-6pps: A blue light illuminated LOV-PAS construct from the LOV-HK sensor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pps | ||||||||||||
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Title | A blue light illuminated LOV-PAS construct from the LOV-HK sensory protein from Brucella abortus (construct 15-273) | ||||||||||||
Components | Blue-light-activated histidine kinase | ||||||||||||
Keywords | SIGNALING PROTEIN / Brucella abortus / LOV domain / sensor histidine kinases / asymmetric activation | ||||||||||||
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 abortus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||||||||
Authors | Rinaldi, J. / Fernandez, I. / Shin, H. / Gunawardana, S. / Otero, L.H. / Cerutti, M.L. / Yang, X. / Klinke, S. / Goldbaum, F.A. | ||||||||||||
Funding support | Argentina, 3items
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Citation | Journal: Mbio / Year: 2021 Title: Dimer Asymmetry and Light Activation Mechanism in Brucella Blue-Light Sensor Histidine Kinase. Authors: Rinaldi, J. / Fernandez, I. / Shin, H. / Sycz, G. / Gunawardana, S. / Kumarapperuma, I. / Paz, J.M. / Otero, L.H. / Cerutti, M.L. / Zorreguieta, A. / Ren, Z. / Klinke, S. / Yang, X. / 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 | 6pps.cif.gz | 437.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pps.ent.gz | 359.4 KB | Display | PDB format |
PDBx/mmJSON format | 6pps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pps_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6pps_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6pps_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 6pps_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/6pps ftp://data.pdbj.org/pub/pdb/validation_reports/pp/6pps | HTTPS FTP |
-Related structure data
Related structure data | 6ph2C 6ph3C 6ph4C 3t50S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31764.271 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria) Strain: 2308 / Gene: BAB2_0652 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YKK7, histidine kinase #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.79 Å3/Da / Density % sol: 55.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 14% (w/v) PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 35284 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.056 / Rrim(I) all: 0.128 / Net I/σ(I): 16.85 |
Reflection shell | Resolution: 2.8→2.87 Å / Num. unique obs: 3187 / CC1/2: 0.653 / Rpim(I) all: 0.685 / Rrim(I) all: 1.542 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3T50 Resolution: 2.8→50 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 235.11 Å2 / Biso min: 38.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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