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Yorodumi- PDB-4lup: Crystal structure of the complex formed by region of E. coli sigm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lup | ||||||
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Title | Crystal structure of the complex formed by region of E. coli sigmaE bound to its -10 element non template strand | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / ECF sigma factor region 2 / Transcription redirection / -10 promoter element / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-templated transcription initiation / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Campagne, S. / Marsh, M.E. / Vorholt, J.A.V. / Allain, F.H.-T. / Capitani, G. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Structural basis for -10 promoter element melting by environmentally induced sigma factors. Authors: Campagne, S. / Marsh, M.E. / Capitani, G. / Vorholt, J.A. / Allain, F.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lup.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lup.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 4lup.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4lup ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4lup | HTTPS FTP |
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-Related structure data
Related structure data | 2maoC 2mapSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12251.906 Da / Num. of mol.: 2 / Fragment: UNP residues 3-92 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoE, BN17_18601, ECs3439, LF82_1962 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0P6M2 #2: DNA chain | Mass: 2121.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: oligonucleotide synthetically generated #3: Chemical | ChemComp-EDO / | #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: 2.02 Å3/Da / Density % sol: 39.09 % |
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Crystal grow | Temperature: 293 K / pH: 6.5 Details: The complex crystallized spontaneously at a concentration of 0.5 mM in the NMR buffer (10 mM Na-Phosphate buffer pH 6.5, 50 mM NaCl), BATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 2M-F / Detector: PIXEL / Date: Apr 30, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: FIXED EXIT DOUBLE, CHANNEL DCM MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→35.075 Å / Num. obs: 64851 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.3 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 28.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MAP Resolution: 1.2→35.075 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.09 / σ(F): 1.36 / Phase error: 17.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3977 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→35.075 Å
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Refine LS restraints |
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LS refinement shell |
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