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- PDB-6ph4: Full length LOV-PAS-HK construct from the LOV-HK sensory protein ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ph4 | ||||||||||||
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Title | Full length LOV-PAS-HK construct from the LOV-HK sensory protein from Brucella abortus (light-adapted, construct 15-489) | ||||||||||||
![]() | Blue-light-activated histidine kinase | ||||||||||||
![]() | TRANSFERASE / PAS SUPERFAMILY / BLUE-LIGHT PHOTORECEPTOR / FMN BINDING / HISTIDINE KINASE | ||||||||||||
Function / homology | ![]() protein histidine kinase activity / response to stimulus / histidine kinase / photoreceptor activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Rinaldi, J. / Otero, L.H. / Fernandez, I. / Goldbaum, F.A. / Shin, H. / Yang, X. / Klinke, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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. #1: ![]() Title: Crystallization and initial X-ray diffraction analysis of the multi-domain Brucella blue light-activated histidine kinase LOV-HK in its illuminated state Authors: Rinaldi, J. / Fernandez, I. / Poth, L.M. / Shepard, W.E. / Savko, M. / Goldbaum, F.A. / Klinke, S. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.1 KB | Display | ![]() |
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PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ph2C ![]() 6ph3C ![]() 6ppsC ![]() 3t50S ![]() 5epvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 54332.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0679 / Plasmid: pET-24a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-ACP / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.7 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 15% (v/v) MPD + 4% (w/v) PEG 4000 + 0.1 M Hepes, pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2017 Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS |
Radiation | Monochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→62.53 Å / Num. obs: 26861 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 92 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.118 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 3.25→3.47 Å / Redundancy: 15.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4778 / CC1/2: 0.609 / Rrim(I) all: 2.774 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3T50 and 5EPV Resolution: 3.25→62.52 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0.47 / Phase error: 38.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→62.52 Å
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Refine LS restraints |
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LS refinement shell |
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