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Yorodumi- PDB-8bft: The E. coli TrpD2 protein YbiB in complex with a C-terminal pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bft | ||||||||||||
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Title | The E. coli TrpD2 protein YbiB in complex with a C-terminal peptide from ObgE | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / TrpD2 / YbiB / ObgE / DNA-binding | ||||||||||||
Function / homology | Function and homology information guanyl ribonucleotide binding / dormancy process / anthranilate phosphoribosyltransferase activity / negative regulation of ribosome biogenesis / tryptophan biosynthetic process / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...guanyl ribonucleotide binding / dormancy process / anthranilate phosphoribosyltransferase activity / negative regulation of ribosome biogenesis / tryptophan biosynthetic process / guanosine tetraphosphate binding / ribosomal large subunit binding / ribosome assembly / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GDP binding / rRNA binding / GTPase activity / GTP binding / magnesium ion binding / protein homodimerization activity / DNA binding / RNA binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | ||||||||||||
Authors | Deckers, B. / Galicia, C. / Versees, W. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2023 Title: YbiB: a novel interactor of the GTPase ObgE. Authors: Deckers, B. / Vercauteren, S. / De Kock, V. / Martin, C. / Lazar, T. / Herpels, P. / Dewachter, L. / Verstraeten, N. / Peeters, E. / Ballet, S. / Michiels, J. / Galicia, C. / Versees, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bft.cif.gz | 249.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bft.ent.gz | 167.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bft_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 8bft_full_validation.pdf.gz | 446.4 KB | Display | |
Data in XML | 8bft_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 8bft_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/8bft ftp://data.pdbj.org/pub/pdb/validation_reports/bf/8bft | HTTPS FTP |
-Related structure data
Related structure data | 8bfrSC S: Starting model for refinement 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: 37553.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ybiB, b0800, JW0785, trpD2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30177 | ||||
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#2: Protein/peptide | Mass: 2498.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) References: UniProt: P42641, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citrate pH 5, 20% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→47.03 Å / Num. obs: 87511 / % possible obs: 92.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.192→1.331 Å / Num. unique obs: 4374 / CC1/2: 0.696 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8BFR Resolution: 1.19→47.03 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5899 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→47.03 Å
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Refine LS restraints |
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LS refinement shell |
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