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- PDB-2yvh: Crystal structure of the operator-binding form of the multi-drug ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yvh | ||||||
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Title | Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor CgmR | ||||||
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![]() | TRANSCRIPTION/DNA / Protein-DNA complex / helix-turn-helix / TetR-family / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Itou, H. / Shirakihara, Y. / Tanaka, I. | ||||||
![]() | ![]() Title: Crystal Structures of the Multidrug Binding Repressor Corynebacteriumglutamicum CgmR in Complex with Inducers and with an Operator Authors: Itou, H. / Watanabe, N. / Yao, M. / Shirakihara, Y. / Tanaka, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.9 KB | Display | ![]() |
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PDB format | ![]() | 142.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.8 KB | Display | ![]() |
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Full document | ![]() | 519.2 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 8 - 171 / Label seq-ID: 8 - 171
NCS ensembles :
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Components
#1: Protein | Mass: 20472.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 4224.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Sequence found in the C.glutamicum genome. #3: DNA chain | Mass: 4335.826 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Sequence found in the C.glutamicum genome. #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.05M Tris-HCl, 0.1M CaCl2, 4% PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2006 / Details: mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97909 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 32512 / Num. obs: 32512 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.48 / Num. unique all: 3252 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.419 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Number: 1323 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.561 Å / Total num. of bins used: 20
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