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Yorodumi- PDB-6za0: Structure of the transcriptional repressor Atu1419 (VanR) in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6za0 | ||||||
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Title | Structure of the transcriptional repressor Atu1419 (VanR) in complex with a fortuitous citrate from agrobacterium fabrum (P21212 space group) | ||||||
Components | Transcriptional regulator, GntR family | ||||||
Keywords | TRANSCRIPTION / repressor | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Agrobacterium fabrum str. C58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Morera, S. / 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 | 6za0.cif.gz | 201.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6za0.ent.gz | 160.7 KB | Display | PDB format |
PDBx/mmJSON format | 6za0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6za0_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6za0_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6za0_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 6za0_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/6za0 ftp://data.pdbj.org/pub/pdb/validation_reports/za/6za0 | HTTPS FTP |
-Related structure data
Related structure data | 6z74SC 6za3C 6za7C 6zabC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27407.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria) Gene: Atu1419 / Production host: Escherichia coli (E. coli) / References: UniProt: A9CJ36 |
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-Non-polymers , 5 types, 339 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-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 | Density Matthews: 2.08 Å3/Da / Density % sol: 40.92 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, AS, Na-citrate |
-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: 0.97857 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→24 Å / Num. obs: 51917 / % possible obs: 97.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.65→1.69 Å / Num. unique obs: 3674 / CC1/2: 0.461 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z74 Resolution: 1.65→23.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.09
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Displacement parameters | Biso mean: 29.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→23.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.67 Å / Total num. of bins used: 50
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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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