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Yorodumi- PDB-8jfv: Crystal structure of Catabolite repressor acivator from E. coli i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jfv | ||||||
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Title | Crystal structure of Catabolite repressor acivator from E. coli in complex with sulisobenzone | ||||||
Components | Catabolite repressor/activator | ||||||
Keywords | TRANSCRIPTION / Transcription factor / bacterial / sulsiobenzone | ||||||
Function / homology | Function and homology information response to fructose / regulation of DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli 536 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Neetu, N. / Sharma, M. / Mahto, J.K. / Kumar, P. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2023 Title: Sulisobenzone is a potent inhibitor of the global transcription factor Cra. Authors: Neetu, N. / Mahto, J.K. / Sharma, M. / Katiki, M. / Dhaka, P. / Roy, P. / Tomar, S. / Narayan, A. / Yernool, D. / Kumar, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jfv.cif.gz | 236.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jfv.ent.gz | 191.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/8jfv ftp://data.pdbj.org/pub/pdb/validation_reports/jf/8jfv | HTTPS FTP |
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-Related structure data
Related structure data | 8jffC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38051.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli 536 (bacteria) / Gene: ECP_0082 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A454A0X5 |
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-Non-polymers , 5 types, 38 molecules
#2: Chemical | ChemComp-I4Y / Mass: 308.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O6S / Feature type: SUBJECT OF INVESTIGATION |
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#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-EPE / |
#5: Chemical | ChemComp-EDO / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: HEPES, MgCl2, PEG 4000 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.973 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→43.08 Å / Num. obs: 11380 / % possible obs: 98.4 % / Redundancy: 1.8 % / CC1/2: 0.969 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.056 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 3.05→3.26 Å / Rmerge(I) obs: 0.395 / Num. unique obs: 2037 / CC1/2: 0.677 / Rpim(I) all: 0.395 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→43.08 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.89 / SU B: 67.492 / SU ML: 0.52 / Cross valid method: THROUGHOUT / ESU R Free: 0.561 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.891 Å2
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Refinement step | Cycle: 1 / Resolution: 3.05→43.08 Å
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