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Yorodumi- PDB-6jyw: Crystal structure of the transcription regulator CadR N81M mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jyw | ||||||
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Title | Crystal structure of the transcription regulator CadR N81M mutant from P. putida in complex with Cadmium(II) and 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: 2.95 Å | ||||||
Authors | Liu, X.C. / Chen, H. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the transcription regulator CadR N81M mutant from P. putida in complex with Cadmium(II) and DNA Authors: Liu, X.C. / Chen, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jyw.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jyw.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/6jyw ftp://data.pdbj.org/pub/pdb/validation_reports/jy/6jyw | HTTPS FTP |
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-Related structure data
Related structure data | 6jgxS S: Starting model for refinement |
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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: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 135 / Label seq-ID: 1 - 135
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-Components
#1: Protein | Mass: 16688.799 Da / Num. of mol.: 2 / Mutation: N81M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: cadR, BIW19_10095, BL240_26950, EFK07_13565 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93TP7 #2: DNA chain | | Mass: 6776.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria) #3: DNA chain | | Mass: 6727.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria) #4: Chemical | ChemComp-CD / |
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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: 4.62 Å3/Da / Density % sol: 73.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, sodium citrate tribasic dihydrate |
-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: Oct 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 17117 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rsym value: 0.09 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JGX Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.192 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.32 / 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: 90.174 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→30 Å
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Refine LS restraints |
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