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- PDB-7la6: THE STRUCTURE OF A SENSOR DOMAIN OF A HISTIDINE KINASE (VxrA) FRO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7la6 | |||||||||
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Title | THE STRUCTURE OF A SENSOR DOMAIN OF A HISTIDINE KINASE (VxrA) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961, N239 deletion mutant | |||||||||
![]() | Sensor histidine kinase | |||||||||
![]() | SIGNALING PROTEIN / VXRA / TWO-COMPONENT SYSTEM / HISTIDINE KINASE / SENSOR DOMAIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | ![]() histidine kinase / phosphorelay sensor kinase activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tan, K. / Wu, R. / Jedrzejczak, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae - A Hairpin-swapped Dimer and its Conformational Change. Authors: Tan, K. / Teschler, J.K. / Wu, R. / Jedrzejczak, R.P. / Zhou, M. / Shuvalova, L.A. / Endres, M.J. / Welk, L.F. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Yildiz, F.H. / Joachimiak, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
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PDB format | ![]() | 82.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r7qSC ![]() 7kb3C ![]() 7kb7C ![]() 7kb9C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24764.877 Da / Num. of mol.: 1 / Mutation: N239 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0565 / Plasmid: PMCSG57 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 78 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M LITHIUM SULFIDE, 0.1 M SODIUM, CACODYLATE:HCL, 30% (W/V) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 5, 2020 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→46 Å / Num. obs: 29036 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 40.01 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.027 / Rrim(I) all: 0.076 / Χ2: 1.574 / Net I/σ(I): 42.2 |
Reflection shell | Resolution: 1.98→2.03 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1416 / CC1/2: 0.747 / Rpim(I) all: 0.302 / Rrim(I) all: 0.845 / Χ2: 0.741 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4R7Q Resolution: 1.98→45.42 Å / SU ML: 0.1838 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.9281 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 46.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→45.42 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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