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Open data
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Basic information
Entry | Database: PDB / ID: 7dob | ||||||
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Title | Crystal structure of Catabolite repressor activator (Apo) | ||||||
![]() | Catabolite repressor/activator | ||||||
![]() | GENE REGULATION / transcription factor / DNA BINDING PROTEIN | ||||||
Function / homology | ![]() response to fructose / transcription cis-regulatory region binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Neetu, N. / Katiki, M. / Kumar, P. | ||||||
![]() | ![]() Title: Crystal structure of Catabolite repressor activator (Apo) Authors: Neetu, N. / Katiki, M. / Kumar, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.6 KB | Display | ![]() |
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PDB format | ![]() | 103.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 947.1 KB | Display | ![]() |
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Full document | ![]() | 946.3 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iksS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 40811.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 536 / UPEC / Gene: ECP_0082 / Production host: ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.3M MgCl2, 0.1M MES, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.8 Å / Num. obs: 12911 / % possible obs: 99.36 % / Redundancy: 8.7 % / CC1/2: 0.99 / Net I/σ(I): 13.84 |
Reflection shell | Resolution: 2.4→2.48 Å / Num. unique obs: 1268 / CC1/2: 0.662 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IKS Resolution: 2.4→36.535 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.99 Å2 / Biso mean: 67.4387 Å2 / Biso min: 26.19 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→36.535 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 14.172 Å / Origin y: 38.3312 Å / Origin z: -15.1159 Å
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Refinement TLS group | Selection details: all |