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Yorodumi- PDB-5ae5: Structures of inactive and activated DntR provide conclusive evid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ae5 | ||||||
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Title | Structures of inactive and activated DntR provide conclusive evidence for the mechanism of action of LysR transcription factors | ||||||
Components | LYSR-TYPE REGULATORY PROTEIN | ||||||
Keywords | TRANSCRIPTION / LYSR-TYPE TRANSCRIPTION REGULATORS / LTTR / TRANSCRIPTION FACTOR / HELIX-TURN-HELIX / DNA BINDING PROTEIN / ROSSMANN-LIKE FOLD / APO-DNTR | ||||||
Function / homology | LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / LysR-type regulatory protein Function and homology information | ||||||
Biological species | BURKHOLDERIA CEPACIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 Å | ||||||
Authors | Lerche, M. / Dian, C. / Round, A. / Lonneborg, R. / Brzezinski, P. / Leonard, G.A. | ||||||
Citation | Journal: Sci.Rep. / Year: 2016 Title: The Solution Configurations of Inactive and Activated Dntr Have Implications for the Sliding Dimer Mechanism of Lysr Transcription Factors. Authors: Lerche, M. / Dian, C. / Round, A. / Lonneborg, R. / Brzezinski, P. / Leonard, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ae5.cif.gz | 238.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ae5.ent.gz | 195.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ae5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ae5_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 5ae5_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 5ae5_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5ae5_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/5ae5 ftp://data.pdbj.org/pub/pdb/validation_reports/ae/5ae5 | HTTPS FTP |
-Related structure data
Related structure data | 5ae4C 1utbS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34872.285 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CEPACIA (bacteria) / Strain: DNT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 / References: UniProt: Q7WT50 #2: Chemical | ChemComp-GOL / #3: 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: 3.54 Å3/Da / Density % sol: 65.39 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.2 M SODIUM POTASSIUM TARTRATE, 0.1 M TRIS-HCL PH 8.0, 5 % (W/V) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS |
Radiation | Monochromator: SI(111) AND SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→47.14 Å / Num. obs: 30522 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.64→2.79 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.1 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UTB Resolution: 2.645→47.142 Å / SU ML: 0.24 / σ(F): 1.38 / Phase error: 21.32 / 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: 93.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.645→47.142 Å
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Refine LS restraints |
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LS refinement shell |
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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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