[English] 日本語
Yorodumi- PDB-4jml: Crystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jml | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) complex. | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT/TOXIN / protein-protein interaction / engineered disulfide / bacteriocin transport / protein transport / PROTEIN TRANSPORT-TOXIN complex | ||||||
Function / homology | Function and homology information extrachromosomal circular DNA / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / protein domain specific binding / protein-containing complex / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Wojdyla, J.A. / Klein, A. / Kleanthous, C. | ||||||
Citation | Journal: Science / Year: 2013 Title: Intrinsically disordered protein threads through the bacterial outer-membrane porin OmpF. Authors: Nicholas G Housden / Jonathan T S Hopper / Natalya Lukoyanova / David Rodriguez-Larrea / Justyna A Wojdyla / Alexander Klein / Renata Kaminska / Hagan Bayley / Helen R Saibil / Carol V ...Authors: Nicholas G Housden / Jonathan T S Hopper / Natalya Lukoyanova / David Rodriguez-Larrea / Justyna A Wojdyla / Alexander Klein / Renata Kaminska / Hagan Bayley / Helen R Saibil / Carol V Robinson / Colin Kleanthous / Abstract: Porins are β-barrel outer-membrane proteins through which small solutes and metabolites diffuse that are also exploited during cell death. We have studied how the bacteriocin colicin E9 (ColE9) ...Porins are β-barrel outer-membrane proteins through which small solutes and metabolites diffuse that are also exploited during cell death. We have studied how the bacteriocin colicin E9 (ColE9) assembles a cytotoxic translocon at the surface of Escherichia coli that incorporates the trimeric porin OmpF. Formation of the translocon involved ColE9's unstructured N-terminal domain threading in opposite directions through two OmpF subunits, capturing its target TolB on the other side of the membrane in a fixed orientation that triggers colicin import. Thus, an intrinsically disordered protein can tunnel through the narrow pores of an oligomeric porin to deliver an epitope signal to the cell to initiate cell death. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jml.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jml.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 4jml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/4jml ftp://data.pdbj.org/pub/pdb/validation_reports/jm/4jml | HTTPS FTP |
---|
-Related structure data
Related structure data | 2372C 2ivzS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44716.629 Da / Num. of mol.: 1 / Mutation: P201C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ECDH1ME8569_0700, EcDH1_2895, tolB / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9R0N0 |
---|---|
#2: Protein/peptide | Mass: 1639.618 Da / Num. of mol.: 1 / Fragment: T-domain, Residues 32-47 / Mutation: A33C / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) References: UniProt: P09883, Hydrolases; Acting on ester bonds |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 80mM calcium chloride, 24% PEG 5000MME, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2013 / Details: mirrors |
Radiation | Monochromator: ACCEL Fixed exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.8 Å / % possible obs: 99 % / Observed criterion σ(I): 1.95 / Redundancy: 6.5 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2→2.12 Å / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.95 / Num. unique all: 8681 / % possible all: 95.3 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ivz Resolution: 2→38.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.179 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 109.66 Å2 / Biso mean: 34.4006 Å2 / Biso min: 16.32 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
|