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- PDB-6zab: Structure of the transcriptional repressor Atu1419 (VanR) from ag... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zab | ||||||
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Title | Structure of the transcriptional repressor Atu1419 (VanR) from agrobacterium fabrum in complex a palindromic DNA (P6422 space group) | ||||||
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![]() | TRANSCRIPTION / repressor | ||||||
Function / homology | ![]() DNA-binding transcription factor activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Morera, S. / Naretto, A. / Vigouroux, A. / Legrand, P. | ||||||
![]() | ![]() Title: Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogen Agrobacterium fabrum. Authors: Vigouroux, A. / Meyer, T. / Naretto, A. / Legrand, P. / Aumont-Nicaise, M. / Di Cicco, A. / Renoud, S. / Dore, J. / Levy, D. / Vial, L. / Lavire, C. / Morera, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.1 KB | Display | ![]() |
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PDB format | ![]() | 94.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.3 KB | Display | ![]() |
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Full document | ![]() | 790.7 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z74SC ![]() 6za0C ![]() 6za3C ![]() 6za7C 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
-Protein / DNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 27407.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: C58 / ATCC 33970 / Gene: Atu1419 / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 3043.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: synthetic construct (others) |
-Non-polymers , 5 types, 27 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / |
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#4: Chemical | ChemComp-CIT / |
#5: Chemical | ChemComp-PEG / |
#6: Chemical | ChemComp-EDO / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: Terbutanol, Na-citrate, MgCl2 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.61 Å / Num. obs: 23104 / % possible obs: 99.7 % / Redundancy: 19.5 % / Biso Wilson estimate: 101.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.8→2.87 Å / Num. unique obs: 1635 / CC1/2: 0.388 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6Z74 Resolution: 2.8→45.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.304 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.222
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Displacement parameters | Biso max: 222 Å2 / Biso mean: 83.94 Å2 / Biso min: 18.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→45.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 40
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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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