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Yorodumi- PDB-4kny: Crystal structure of the response regulator KdpE complexed to DNA... -
+Open data
-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 | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR/DNA / receiver domain / DNA-binding domain / TRANSCRIPTION REGULATOR-DNA complex | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.945 Å | ||||||
Authors | Kumar, S. / Narayanan, A. / Yernool, D.A. | ||||||
Citation | Journal: Nat Commun / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kny.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kny.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/4kny ftp://data.pdbj.org/pub/pdb/validation_reports/kn/4kny | HTTPS FTP |
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-Related structure data
Related structure data | 4kfcC 4l85C 1zh4S 3zq7S 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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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.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0694, JW5096, kdpE / Production host: Escherichia coli (E. coli) / References: UniProt: P21866 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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