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Yorodumi- PDB-6jgf: Crystal structure of Se-Met CadR from P. putida with a 21 residue... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jgf | ||||||
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Title | Crystal structure of Se-Met CadR from P. putida with a 21 residue C-terminal truncation | ||||||
Components | CadR | ||||||
Keywords | TRANSCRIPTION / CadR / MerR family / cadmium regulator | ||||||
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 / SAD / Resolution: 2.15 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 | 6jgf.cif.gz | 33.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jgf.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jgf_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 6jgf_full_validation.pdf.gz | 423.7 KB | Display | |
Data in XML | 6jgf_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 6jgf_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/6jgf ftp://data.pdbj.org/pub/pdb/validation_reports/jg/6jgf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14583.201 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.056M Sodium phosphate monobasic, 1.344M Potassium phosphate dibasic |
-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: May 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 7330 / % possible obs: 99.1 % / Redundancy: 20 % / Rsym value: 0.11 / Net I/σ(I): 72.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 8.1 / Num. unique obs: 705 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.84 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.24 / 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: 49.411 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→30 Å
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Refine LS restraints |
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