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Yorodumi- PDB-6jgw: Crystal structure of the transcriptional regulator CadR from P. p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jgw | ||||||
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Title | Crystal structure of the transcriptional regulator CadR from P. putida in complex with DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / CadR / MerR family / cadmium regulator / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liu, X.C. / Gan, J.H. / Chen, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: Selective cadmium regulation mediated by a cooperative binding mechanism in CadR. Authors: Liu, X. / Hu, Q. / Yang, J. / Huang, S. / Wei, T. / Chen, W. / He, Y. / Wang, D. / Liu, Z. / Wang, K. / Gan, J. / Chen, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jgw.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jgw.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jgw_validation.pdf.gz | 440.4 KB | Display | wwPDB validaton report |
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Full document | 6jgw_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 6jgw_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 6jgw_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/6jgw ftp://data.pdbj.org/pub/pdb/validation_reports/jg/6jgw | HTTPS FTP |
-Related structure data
Related structure data | 6jgfC 6jgvSC 6jgxC 6jniC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 116 / Label seq-ID: 1 - 116
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-Components
#1: Protein | Mass: 16671.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: cadR, BIW19_10095, BL240_26950 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93TP7 #2: DNA chain | | Mass: 8338.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria) #3: DNA chain | | Mass: 8254.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria) #4: 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: 3.15 Å3/Da / Density % sol: 60.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: MPEG 2000, potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2012 |
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→30 Å / Num. obs: 15413 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rsym value: 0.1 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1527 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JGV Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 15.016 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R: 0.648 / ESU R Free: 0.331 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.28 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→30 Å
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Refine LS restraints |
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