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Yorodumi- PDB-3d6y: Crystal structure of R275E mutant of BMRR bound to DNA and berberine -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d6y | ||||||
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Title | Crystal structure of R275E mutant of BMRR bound to DNA and berberine | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR/DNA / MULTIDRUG RESISTANCE / TRANSCRIPTION REGULATION / PROTEIN-DNA COMPLEX / Activator / DNA-binding / TRANSCRIPTION REGULATOR-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å | ||||||
Authors | Newberry, K.J. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d6y.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d6y.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 3d6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3d6y_validation.pdf.gz | 739.2 KB | Display | wwPDB validaton report |
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Full document | 3d6y_full_validation.pdf.gz | 755.4 KB | Display | |
Data in XML | 3d6y_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3d6y_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/3d6y ftp://data.pdbj.org/pub/pdb/validation_reports/d6/3d6y | HTTPS FTP |
-Related structure data
Related structure data | 3d6zC 3d70C 3d71C 1r8dS 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
#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: 33450.121 Da / Num. of mol.: 1 / Fragment: residues 1-278 / Mutation: R275E, 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39075 | ||
#3: Chemical | ChemComp-BER / | ||
#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: 5.081581 Å3/Da / Density % sol: 75.794937 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0 M Sodium Malonate, 0.05% Jeffamine-M600, pH 7.0, 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: ALS / Beamline: 8.2.1 / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2004 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→86.1 Å / Num. obs: 23429 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 78.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.057 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.7→2.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3331 / Rsym value: 0.544 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB entry 1R8D Resolution: 2.7→86.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1684928.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.1095 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→86.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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