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- PDB-4kny: Crystal structure of the response regulator KdpE complexed to DNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kny | ||||||
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Title | Crystal structure of the response regulator KdpE complexed to DNA in an active-like conformation | ||||||
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![]() | TRANSCRIPTION REGULATOR/DNA / receiver domain / DNA-binding domain / TRANSCRIPTION REGULATOR-DNA complex | ||||||
Function / homology | ![]() phosphorelay response regulator activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, S. / Narayanan, A. / Yernool, D.A. | ||||||
![]() | ![]() Title: An asymmetric heterodomain interface stabilizes a response regulator-DNA complex. Authors: Narayanan, A. / Kumar, S. / Evrard, A.N. / Paul, L.N. / Yernool, D.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 | ![]() | 128.3 KB | Display | ![]() |
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PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 452 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4kfcC ![]() 4l85C ![]() 1zh4S ![]() 3zq7S 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: 25495.242 Da / Num. of mol.: 2 / Fragment: UNP residues 3-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 9025.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized #3: DNA chain | | Mass: 9418.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 71.16 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10-15% PEG 4K, 0.1 M sodium acetate buffer (pH 5.5), 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→66.57 Å / Num. all: 26044 / Num. obs: 25980 / % possible obs: 99.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.95→3.05 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1ZH4, 3ZQ7 Resolution: 2.945→66.57 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 24.55 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.945→66.57 Å
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Refine LS restraints |
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LS refinement shell |
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