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- PDB-4n9i: Crystal Structure of Transcription regulation protein CRP complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4n9i | ||||||
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Title | Crystal Structure of Transcription regulation protein CRP complexed with cGMP | ||||||
![]() | Catabolite gene activator | ||||||
![]() | TRANSCRIPTION REGULATOR / DNA Binding | ||||||
Function / homology | ![]() transferase activity / DNA-binding transcription factor activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, B.-J. / Seok, S.-H. / Im, H. / Yoon, H.-J. | ||||||
![]() | ![]() Title: Structures of inactive CRP species reveal the atomic details of the allosteric transition that discriminates cyclic nucleotide second messengers. Authors: Seok, S.H. / Im, H. / Won, H.S. / Seo, M.D. / Lee, Y.S. / Yoon, H.J. / Cha, M.J. / Park, J.Y. / Lee, B.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.4 KB | Display | ![]() |
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PDB format | ![]() | 140 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4n9hC ![]() 3hifS C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23672.439 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PCG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 400, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 28, 2012 | |||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.19→50.01 Å / Num. obs: 45063 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.066 | |||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 12.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HIF Resolution: 2.19→42.57 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.008 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.957 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→42.57 Å
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Refine LS restraints |
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