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Yorodumi- PDB-6ph3: LOV-PAS construct from the LOV-HK sensory protein from Brucella a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ph3 | ||||||||||||
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Title | LOV-PAS construct from the LOV-HK sensory protein from Brucella abortus (dark-adapted, construct 15-273) | ||||||||||||
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 / histidine kinase / photoreceptor activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Brucella melitensis biotype 1 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||||||||
Authors | Rinaldi, J. / Otero, L.H. / Fernandez, I. / Goldbaum, F.A. / Shin, H. / Yang, X. / Klinke, S. | ||||||||||||
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 | 6ph3.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ph3.ent.gz | 170.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ph3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/6ph3 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6ph3 | HTTPS FTP |
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-Related structure data
Related structure data | 6ph2C 6ph4C 6ppsC 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: 30321.566 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria) Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0679 / Plasmid: pET-24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q8YC53, 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: 2.84 Å3/Da / Density % sol: 56.65 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016 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: 2.74→47.7 Å / Num. obs: 36012 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 83.44 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.13 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.74→2.9 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5428 / CC1/2: 0.874 / Rrim(I) all: 0.91 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T50 Resolution: 2.74→47.7 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.865 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.017 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.871 / SU Rfree Blow DPI: 0.342 / SU Rfree Cruickshank DPI: 0.353
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Displacement parameters | Biso mean: 74.45 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.74→47.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.74→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
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