+Open data
-Basic information
Entry | Database: PDB / ID: 1i6a | ||||||
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Title | CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF OXYR | ||||||
Components | HYDROGEN PEROXIDE-INDUCIBLE GENES ACTIVATOR | ||||||
Keywords | TRANSCRIPTION / OxyR regulatory domain / oxidized form | ||||||
Function / homology | Function and homology information response to nitrosative stress / regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / response to oxidative stress / DNA-binding transcription factor activity / DNA damage response / regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Choi, H. / Kim, S. / Ryu, S. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Structural basis of the redox switch in the OxyR transcription factor. Authors: Choi, H. / Kim, S. / Mukhopadhyay, P. / Cho, S. / Woo, J. / Storz, G. / Ryu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i6a.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i6a.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i6a_validation.pdf.gz | 424.8 KB | Display | wwPDB validaton report |
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Full document | 1i6a_full_validation.pdf.gz | 427 KB | Display | |
Data in XML | 1i6a_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1i6a_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/1i6a ftp://data.pdbj.org/pub/pdb/validation_reports/i6/1i6a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24394.307 Da / Num. of mol.: 1 / Fragment: REGULATORY DOMAIN / Mutation: C143A, C180A, C259A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0ACQ4 |
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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: 2.15 Å3/Da / Density % sol: 42.7 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 K | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 9049 / Rsym value: 0.064 |
Reflection | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.064 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: reduced form of OxyR Resolution: 2.3→100 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→100 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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