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Yorodumi- PDB-6zab: Structure of the transcriptional repressor Atu1419 (VanR) from ag... -
+Open data
-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) | ||||||
Components |
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Keywords | TRANSCRIPTION / repressor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium fabrum (bacteria) Agrobacterium fabrum str. C58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Morera, S. / Naretto, A. / Vigouroux, A. / Legrand, P. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zab.cif.gz | 125.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zab.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 6zab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/6zab ftp://data.pdbj.org/pub/pdb/validation_reports/za/6zab | HTTPS FTP |
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-Related structure data
Related structure data | 6z74SC 6za0C 6za3C 6za7C S: Starting model for refinement C: citing same article (ref.) |
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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
-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.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: Atu1419 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CJ36 |
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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.) Agrobacterium fabrum str. C58 (bacteria) Production host: synthetic construct (others) |
-Non-polymers , 5 types, 27 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å |
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: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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