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Yorodumi- PDB-1zgz: Crystal Structure Of The Receiver Domain Of TMAO Respiratory Syst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zgz | ||||||
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Title | Crystal Structure Of The Receiver Domain Of TMAO Respiratory System Response Regulator TorR | ||||||
Components | TorCAD operon transcriptional regulatory protein torR | ||||||
Keywords | TRANSCRIPTION / Two-Component System / Gene Regulation / Transcription Factor / TMAO Respiratory System / Doubly Wound Five-Stranded Beta-Alpha Fold | ||||||
Function / homology | Function and homology information phosphorelay response regulator activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Toro-Roman, A. / Wu, T. / Stock, A.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2005 Title: A common dimerization interface in bacterial response regulators KdpE and TorR. Authors: Toro-Roman, A. / Wu, T. / Stock, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zgz.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zgz.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/1zgz ftp://data.pdbj.org/pub/pdb/validation_reports/zg/1zgz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 14002.429 Da / Num. of mol.: 4 / Fragment: N-Terminal Receiver Domain (residues 1-122) / Mutation: L122Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: torR / Plasmid: pEF26 (pJES307 derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: P38684 #2: Chemical | #3: Chemical | ChemComp-GOL / | #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: 1.7 Å3/Da / Density % sol: 28.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 2000 MME, Ammonium Sulfate, Sodium Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97888 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2003 |
Radiation | Monochromator: KOHZU Double Crystal Monochromator With A Sagittally Focused Second Crystal. Crystal Type Is Si(111). Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97888 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 35665 / Num. obs: 34815 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 17.1 Å2 / Rsym value: 0.084 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2834 / Rsym value: 0.367 / % possible all: 80.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.444 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.166 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.472 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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