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Yorodumi- PDB-3d71: Crystal structure of E253Q BMRR bound to 22 base pair promoter site -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d71 | ||||||
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Title | Crystal structure of E253Q BMRR bound to 22 base pair promoter site | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR/DNA / TRANSCRIPTION REGULATOR / PROTEIN-DNA COMPLEX / MULTIDRUG BINDING PROTEIN / MERR FAMILY / WINGED-HELIX / Activator / DNA-binding / Transcription regulation / TRANSCRIPTION REGULATOR-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Newberry, K.J. / Huffman, J.L. / Brennan, R.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket and Transcription Activation through Tyrosine Expulsion Authors: Newberry, K.J. / Huffman, J.L. / Miller, M.C. / Vazquez-Laslop, N. / Neyfakh, A.A. / Brennan, R.G. #1: Journal: J.Biol.Chem. / Year: 2004 Title: The Structural Mechanism for Transcription Activation by Merr Family Member Multidrug Transporter Activation, N Terminus. Authors: Newberry, K.J. / 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 | 3d71.cif.gz | 89.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d71.ent.gz | 64.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d71_validation.pdf.gz | 493.4 KB | Display | wwPDB validaton report |
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Full document | 3d71_full_validation.pdf.gz | 500.5 KB | Display | |
Data in XML | 3d71_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3d71_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d71 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d71 | HTTPS FTP |
-Related structure data
Related structure data | 3d6yC 3d6zC 3d70C 1exjS 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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1 |
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Unit cell |
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-Components
-DNA chain / Protein , 2 types, 2 molecules MA
#1: DNA chain | Mass: 7362.729 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Protein | Mass: 33477.219 Da / Num. of mol.: 1 / Fragment: residues 1-278 / Mutation: E253Q, A277L, E278D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: bmrR, bmr1R / Plasmid: PBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P39075 |
-Non-polymers , 6 types, 66 molecules
#3: Chemical | ChemComp-ZN / | ||||||
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#4: Chemical | ChemComp-FLC / | ||||||
#5: Chemical | #6: Chemical | ChemComp-ETF / | #7: Chemical | ChemComp-IMD / #8: 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: 5.3 Å3/Da / Density % sol: 79 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: SODIUM CITRATE, IMIDAZOLE, TRIFLUOROETHANOL, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 2001 / Details: MIRRORS |
Radiation | Monochromator: SILICON SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.2 Å / Num. obs: 20900 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 45.3 Å2 / Rsym value: 0.051 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.8→2.86 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.454 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EXJ Resolution: 2.8→47.17 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.42 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→47.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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