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Yorodumi- PDB-4kfc: Crystal structure of a hyperactive mutant of response regulator K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kfc | ||||||
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Title | Crystal structure of a hyperactive mutant of response regulator KdpE complexed to its promoter DNA | ||||||
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: 2.53 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 | 4kfc.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kfc.ent.gz | 103.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/4kfc ftp://data.pdbj.org/pub/pdb/validation_reports/kf/4kfc | HTTPS FTP |
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-Related structure data
Related structure data | 4knyC 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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Details | The present structures with two protein molecules bound to dsDNA, represents the biological assemble. |
-Components
#1: Protein | Mass: 25437.207 Da / Num. of mol.: 2 / Fragment: UNP residues 3-225 / Mutation: E216A 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: 4.28 Å3/Da / Density % sol: 71.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 3-5% PEG 4K, 0.1 M sodium acetate buffer (pH 5.5), 0.1 M MgCl2, 2mM L-proline, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: 2.53→44.43 Å / Num. all: 40355 / Num. obs: 40336 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.48 |
Reflection shell | Resolution: 2.53→2.62 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.4 / Num. unique all: 40355 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZH4 and 3ZQ7 Resolution: 2.53→44.32 Å / SU ML: 0.31 / σ(F): 1.33 / Phase error: 25.02 / 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: 2.53→44.32 Å
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Refine LS restraints |
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LS refinement shell |
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