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Open data
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Basic information
Entry | Database: PDB / ID: 1odd | ||||||
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Title | OMPR C-TERMINAL DOMAIN (OMPR-C) FROM ESCHERICHIA COLI | ||||||
![]() | TRANSCRIPTIONAL REGULATORY PROTEIN OMPR | ||||||
![]() | GENE REGULATORY PROTEIN / POSITIVE RESPONSE REGULATOR / DNA BINDING DOMAIN | ||||||
Function / homology | ![]() phosphorelay response regulator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kondou, H. / Nakagawa, A. / Tanaka, I. | ||||||
![]() | ![]() Title: Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site. Authors: Kondo, H. / Nakagawa, A. / Nishihira, J. / Nishimura, Y. / Mizuno, T. / Tanaka, I. #1: ![]() Title: Crystallization and X-Ray Studies of the DNA-Binding Domain of OmpR Protein, a Positive Regulator Involved in Activation of Osmoregulatory Genes in Escherichia Coli Authors: Kondo, H. / Miyaji, T. / Suzuki, M. / Tate, S. / Mizuno, T. / Nishimura, Y. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32.6 KB | Display | ![]() |
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PDB format | ![]() | 21.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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: 13405.311 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD. | |||||||||||||||
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Crystal grow | pH: 6 Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M SODIUM CACODYLATE, 0.2M SODIUM ACETATE, 20%(W/V) PEG8000, PH 6.0; THEN SOAKED IN 35% PEG8000 WITH CRYSTALLIZATION BUFFER. | |||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / Details: Kondo, H., (1994) J.Mol.Biol., 235, 780. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: MIRROR, COLLIMATOR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 6153 / % possible obs: 98.1 % / Observed criterion σ(I): 4 / Redundancy: 5.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 1.9 / % possible all: 96.3 |
Reflection | *PLUS Num. measured all: 31412 |
Reflection shell | *PLUS % possible obs: 96.3 % |
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Processing
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Refinement | Method to determine structure: MAD WITH SE-MET MUTANT / Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: PROGRAM X-PLOR BY BRUNGER ALSO WAS USED.
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Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||
Refine LS restraints | *PLUS
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