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Yorodumi- PDB-8jff: Crystal structure of Catabolite repressor acivator from E. coli i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jff | ||||||
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Title | Crystal structure of Catabolite repressor acivator from E. coli in complex with HEPES | ||||||
Components | Catabolite repressor/activator | ||||||
Keywords | GENE REGULATION / Cra / HEPES / DNA BINDING PROTEIN | ||||||
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: 2.89 Å | ||||||
Authors | Neetu, N. / Katiki, M. / 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 | 8jff.cif.gz | 235.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jff.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 8jff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/8jff ftp://data.pdbj.org/pub/pdb/validation_reports/jf/8jff | HTTPS FTP |
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-Related structure data
Related structure data | 8jfvC 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
#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 #2: Chemical | #3: Water | ChemComp-HOH / | 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 / 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: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→108.9 Å / Num. obs: 12352 / % possible obs: 90.1 % / Redundancy: 1.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.046 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.89→3.06 Å / Rmerge(I) obs: 0.341 / Num. unique obs: 2133 / CC1/2: 0.883 / Rpim(I) all: 0.341 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→54.51 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.894 / SU B: 42 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / 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 Å2
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Refinement step | Cycle: 1 / Resolution: 2.89→54.51 Å
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