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Yorodumi- PDB-2z2s: Crystal Structure of Rhodobacter sphaeroides SigE in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z2s | ||||||
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Title | Crystal Structure of Rhodobacter sphaeroides SigE in complex with the anti-sigma ChrR | ||||||
Components |
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Keywords | TRANSCRIPTION / ECF sigma factor / anti-sigma factor / cupin fold / DNA-binding / Transcription regulation / Activator / Metal-binding / Zinc binding transcription factor | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-templated transcription initiation / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Darst, S.A. / Campbell, E.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria. Authors: Campbell, E.A. / Greenwell, R. / Anthony, J.R. / Wang, S. / Lim, L. / Das, K. / Sofia, H.J. / Donohue, T.J. / Darst, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z2s.cif.gz | 266 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z2s.ent.gz | 222.7 KB | Display | PDB format |
PDBx/mmJSON format | 2z2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z2s_validation.pdf.gz | 519.2 KB | Display | wwPDB validaton report |
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Full document | 2z2s_full_validation.pdf.gz | 609.9 KB | Display | |
Data in XML | 2z2s_validation.xml.gz | 65.3 KB | Display | |
Data in CIF | 2z2s_validation.cif.gz | 89.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/2z2s ftp://data.pdbj.org/pub/pdb/validation_reports/z2/2z2s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21309.201 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: rpoE / Plasmid: pET28a derivitive / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3IYV6 #2: Protein | Mass: 21804.225 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: chrR / Plasmid: pET28a derivitive / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40685 #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M MES, 0.2 M ammonium sulfate, 14-18% polyethylene glycol monomethylether 5000 (PEG5KMME), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97969 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2003 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97969 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. obs: 24975 / % possible obs: 75.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 2.14 / Num. unique all: 2887 / Rsym value: 0.079 / % possible all: 60.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: maximum likelihood
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Refinement step | Cycle: LAST / Resolution: 2.7→25 Å
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Refine LS restraints |
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