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- PDB-3ikt: Crystal structure of a Rex-family repressor/DNA/NAD+ complex from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ikt | ||||||
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Title | Crystal structure of a Rex-family repressor/DNA/NAD+ complex from Thermus aquaticus | ||||||
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![]() | DNA BINDING PROTEIN/DNA / redox-sensing / winged helix / Rossmann fold / Nicotinamide Adenine Dinucleotide / NAD / Rex / Thermus aquaticus / DNA BINDING PROTEIN / Cytoplasm / DNA-binding / Repressor / Transcription / Transcription regulation / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | ![]() response to redox state / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McLaughlin, K.J. / Kielkopf, C.L. | ||||||
![]() | ![]() Title: Structural basis for NADH/NAD+ redox sensing by a Rex family repressor. Authors: McLaughlin, K.J. / Strain-Damerell, C.M. / Xie, K. / Brekasis, D. / Soares, A.S. / Paget, M.S. / Kielkopf, C.L. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.6 KB | Display | ![]() |
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PDB format | ![]() | 94.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.4 KB | Display | ![]() |
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Full document | ![]() | 796 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ikvC ![]() 3il2C ![]() 1xcbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | BIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT. |
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Components
#1: Protein | Mass: 22730.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: DNA chain | Mass: 6753.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 22bp dsDNA obtained from IDT #3: Chemical | ChemComp-NAD / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20-30% PEG 400, 0.1M Na Cacodylate pH 6.0, 0.2M CaCl2, 5-10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
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 4 / Detector: CCD Details: Vertically collimating mirror followed by a channel-cut Si(111) crystal monochromator and a double focusing toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 40822 / % possible obs: 97.6 % / Redundancy: 10.7 % / Rsym value: 0.086 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.26→2.37 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 7.2 / Rsym value: 0.401 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1XCB Resolution: 2.26→20 Å / Cross valid method: MAXIMUM LIKELIHOOD / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.26→20 Å
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Refine LS restraints |
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