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Yorodumi- PDB-8p9r: Structure of the periplasmic domain of ExbD from E. coli in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p9r | |||||||||
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Title | Structure of the periplasmic domain of ExbD from E. coli in complex with TonB | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ton / TonB-binding / ExbB-integrated / periplasmic | |||||||||
Function / homology | Function and homology information receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / bacteriocin transport / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / bacteriocin transport / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein stabilization / protein domain specific binding / protein homodimerization activity / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | |||||||||
Authors | Zinke, M. / Mechaly, A. / Lejeune, M. / Haouz, A. / Izadi-Pruneyre, N. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake. Authors: Zinke, M. / Lejeune, M. / Mechaly, A. / Bardiaux, B. / Boneca, I.G. / Delepelaire, P. / Izadi-Pruneyre, N. #1: Journal: Biorxiv / Year: 2023 Title: Ton Motor Conformational Switch and Peptidoglycan Role in Bacterial Nutrient Uptake. Authors: Zinke, M. / Lejeune, M. / Mechaly, A. / Bardiaux, B. / Boneca, I.G. / Delepelaire, P. / Izadi-Pruneyre, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p9r.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p9r.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 8p9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/8p9r ftp://data.pdbj.org/pub/pdb/validation_reports/p9/8p9r | HTTPS FTP |
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-Related structure data
Related structure data | 8pekC 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: 9071.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: exbD, b3005, JW2973 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABV2 #2: Protein/peptide | | Mass: 2481.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P02929 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 10 %w/v Glycerol, 3M ammonium sulfate |
-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: 1.3799 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3799 Å / Relative weight: 1 |
Reflection | Resolution: 1.52→39.07 Å / Num. obs: 46421 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.99 / Rrim(I) all: 0.061 / Rsym value: 0.0585 / Net I/σ(I): 21.45 |
Reflection shell | Resolution: 1.52→1.61 Å / Mean I/σ(I) obs: 2.45 / Num. unique obs: 7485 / CC1/2: 0.897 / Rrim(I) all: 0.816 / Rsym value: 0.784 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→30.64 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 26.75 / 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: 1.52→30.64 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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