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- PDB-3f8c: Crystal structure of multidrug binding transcriptional regulator ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f8c | ||||||
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Title | Crystal structure of multidrug binding transcriptional regulator LmrR complexed with Hoechst 33342 | ||||||
![]() | Transcriptional regulator, PadR-like family | ||||||
![]() | TRANSCRIPTION REGULATOR / Winged helix turn helix | ||||||
Function / homology | ![]() Transcription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Madoori, P.K. / Agustiandari, H. / Driessen, A.J.M. / Thunnissen, A.-M.W.H. | ||||||
![]() | ![]() Title: Structure of the transcriptional regulator LmrR and its mechanism of multidrug recognition. Authors: Madoori, P.K. / Agustiandari, H. / Driessen, A.J. / Thunnissen, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.4 KB | Display | ![]() |
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PDB format | ![]() | 24.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 628.5 KB | Display | ![]() |
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Full document | ![]() | 629.7 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f8bSC ![]() 3f8fC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14764.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: MG1363 / Gene: lmrR / Plasmid: pNSC8048 / Production host: ![]() |
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#2: Chemical | ChemComp-HT1 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.55 % / Mosaicity: 0.49 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 25% PEG 1500, 0.1M succinic acid/phosphate/glycine (SPG buffer), pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.27 Å / Num. all: 6957 / Num. obs: 6957 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rsym value: 0.052 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.22 / Num. unique all: 969 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 32.66 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3F8B Resolution: 2.2→49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.209 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.813 / SU B: 13.411 / SU ML: 0.154 / SU R Cruickshank DPI: 0.262 / SU Rfree: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.66 Å2 / Biso mean: 21.644 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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