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- PDB-5is1: Crystal structure of the extracellular domain of sensor histidine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5is1 | ||||||
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Title | Crystal structure of the extracellular domain of sensor histidine kinase YycG from Staphylococcus aureus at 2.0 Angstrom resolution | ||||||
![]() | Histidine kinase | ||||||
![]() | TRANSFERASE / PAS/PDC domain / sensor histidine kinase / nest motif / membrane protein | ||||||
Function / homology | ![]() osmosensory signaling via phosphorelay pathway / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020 / ATP binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, T. / Choi, J. / Lee, S. / Kim, K.K. | ||||||
![]() | ![]() Title: Structural Studies on the Extracellular Domain of Sensor Histidine Kinase YycG from Staphylococcus aureus and Its Functional Implications Authors: Kim, T. / Choi, J. / Lee, S. / Yeo, K.J. / Cheong, H.K. / Kim, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.2 KB | Display | ![]() |
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PDB format | ![]() | 54.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.8 KB | Display | ![]() |
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Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: 17399.508 Da / Num. of mol.: 1 / Fragment: Extracellular domai, UNP residues 33-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: walK, walK_1, AL493_01420, AL498_11610, AL508_14645, AM595_00105, ASU36_11995, AUC48_00105, AUC49_00105, AUC50_00105, BN1321_430109, CH51_00105, EQ80_000105, ER12_000105, ERS092844_02460, ...Gene: walK, walK_1, AL493_01420, AL498_11610, AL508_14645, AM595_00105, ASU36_11995, AUC48_00105, AUC49_00105, AUC50_00105, BN1321_430109, CH51_00105, EQ80_000105, ER12_000105, ERS092844_02460, ERS093009_00906, ERS179246_01836, ERS195423_01765, ERS365775_01678, ERS410449_00558, ERS411009_01438, ERS411017_01103, ERS445051_00023, ERS445052_00659, FE68_05490, NI36_00110, RL02_04070, RT87_00105, SA7112_13655, SASCBU26_00023 Production host: ![]() ![]() References: UniProt: V5YQR2, UniProt: Q2G2U4*PLUS, histidine kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.85 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 6 Details: 40-55% (w/v) PEG 400, 100mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 11, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.998→20 Å / Num. obs: 9779 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 41.92 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 71.355 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.55 Å2 / Biso mean: 54.0375 Å2 / Biso min: 18.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.998→19.829 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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