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- PDB-8yz7: Crystal structure of DdrI, a CRP family protein from Deinococcus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yz7 | ||||||
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Title | Crystal structure of DdrI, a CRP family protein from Deinococcus radiodurans | ||||||
![]() | Transcriptional regulator, FNR/CRP family | ||||||
![]() | TRANSCRIPTION / DNA binding / gene regulation | ||||||
Function / homology | : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, Y. / Wang, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans. Authors: Wang, Y. / Hu, J. / Gao, X. / Cao, Y. / Ye, S. / Chen, C. / Wang, L. / Xu, H. / Guo, M. / Zhang, D. / Zhou, R. / Hua, Y. / Zhao, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.3 KB | Display | ![]() |
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PDB format | ![]() | 66 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.3 KB | Display | ![]() |
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Full document | ![]() | 418.7 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zcwS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 22001.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The GenBank accession number A2G07_08515 Source: (gene. exp.) ![]() Gene: DR_0997 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Bis-Tris, KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 1, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. obs: 18623 / % possible obs: 99.9 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.075 / Net I/σ(I): 23.77 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZCW Resolution: 2→30 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -8.821 Å / Origin y: -33.502 Å / Origin z: -9.543 Å
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Refinement TLS group |
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