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Yorodumi- PDB-1exi: CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTIL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1exi | ||||||
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Title | CRYSTAL STRUCTURE OF TRANSCRIPTION ACTIVATOR BMRR, FROM B. SUBTILIS, BOUND TO 21 BASE PAIR BMR OPERATOR AND TPSB | ||||||
Components |
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Keywords | Transcription/DNA / Protein-DNA complex / MerR-family transcription activator / multidrug-binding protein / Transcription-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.12 Å | ||||||
Authors | Zheleznova-Heldwein, E.E. / Brennan, R.G. | ||||||
Citation | Journal: Nature / Year: 2001 Title: Crystal structure of the transcription activator BmrR bound to DNA and a drug. Authors: Heldwein, E.E. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1exi.cif.gz | 81.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1exi.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1exi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/1exi ftp://data.pdbj.org/pub/pdb/validation_reports/ex/1exi | HTTPS FTP |
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-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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Details | The biological assembly is a dimer constructed from chain A by generating a two-fold symmetry partner. / The biological assembly is a DNA duplex constructed from chain B by generating a two-fold symmetry partner. |
-Components
#1: DNA chain | Mass: 6440.148 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Protein | Mass: 32621.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / References: UniProt: P39075 | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: 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: 5.61 Å3/Da / Density % sol: 78.09 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1 M imidazole, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||
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: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 16, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.12→60.4 Å / Num. obs: 44719 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 3.12→3.6 Å / Redundancy: 2 % / Rmerge(I) obs: 0.278 / % possible all: 78 |
-Processing
Software |
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Refinement | Resolution: 3.12→16 Å / Cross valid method: throughtout / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.12→16 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 1 / % reflection Rfree: 4.6 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 1.5 |