+Open data
-Basic information
Entry | Database: PDB / ID: 6lki | ||||||
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Title | Two-component system protein mediate signal transduction | ||||||
Components |
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Keywords | SIGNALING PROTEIN/TRANSFERASE / two-component system / G6P sensor / signal transduction / SIGNALING PROTEIN / SIGNALING PROTEIN-TRANSFERASE complex | ||||||
Function / homology | Function and homology information histidine kinase / phosphorelay sensor kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.781 Å | ||||||
Authors | Wang, M. / Tao, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Interface switch mediates signal transmission in a two-component system. Authors: Wang, M. / Guo, Q. / Zhu, K. / Fang, B. / Yang, Y. / Teng, M. / Li, X. / Tao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lki.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lki.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 6lki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/6lki ftp://data.pdbj.org/pub/pdb/validation_reports/lk/6lki | HTTPS FTP |
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-Related 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: 33898.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: E4U00_07700, EP54_06205, EQ90_12025, HMPREF3211_02751, NCTC10654_00249, NCTC10702_00414, RK64_01575 Production host: Escherichia coli (E. coli) / References: UniProt: X5DVD1 |
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#2: Protein | Mass: 20444.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / Gene: hptS, SAOUHSC_00185 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G1E0, histidine kinase |
#3: Chemical | ChemComp-MLA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 60% v/v Tacsimate pH 7.0, 0.1 M BIS-TRIS propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. obs: 57600 / % possible obs: 98.1 % / Redundancy: 12.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.053 / Rrim(I) all: 0.185 / Net I/σ(I): 15.83 |
Reflection shell | Resolution: 1.78→1.84 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 4922 / CC1/2: 0.779 / Rpim(I) all: 0.419 / Rrim(I) all: 1.345 / % possible all: 85.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.781→48.749 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.07 Å2 / Biso mean: 43.9828 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.781→48.749 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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