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Yorodumi- PDB-3zq7: The Structure of DNA-binding domain of response regulator from Es... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zq7 | ||||||
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Title | The Structure of DNA-binding domain of response regulator from Escherichia coli K-12 | ||||||
Components | KDP OPERON TRANSCRIPTIONAL REGULATORY PROTEIN KDPE | ||||||
Keywords | TRANSCRIPTION / RESPONSE REGULATOR | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Patil, D.N. / Tomar, S. / Kumar, P. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Structure-Function Studies of DNA Binding Domain of Response Regulator Kdpe Reveals Equal Affinity Interactions at DNA Half-Sites. Authors: Narayanan, A. / Paul, L.N. / Tomar, S. / Patil, D.N. / Kumar, P. / 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 | 3zq7.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zq7.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/3zq7 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/3zq7 | HTTPS FTP |
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-Related structure data
Related structure data | 2oqrS S: Starting model for refinement |
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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: 11781.595 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN OF KDPE, RESIDUES 124-225 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Variant: MG1655 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21866 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.82 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: LITHIUM SULFATE, 0.1M HEPES PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 3378 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 40.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.5→35 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 9.1 / % possible all: 77.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OQR Resolution: 2.52→35.24 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.868 / SU B: 27.097 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.763 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→35.24 Å
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Refine LS restraints |
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