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- PDB-2ivz: Structure of TolB in complex with a peptide of the colicin E9 T- ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ivz | ||||||
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Title | Structure of TolB in complex with a peptide of the colicin E9 T- domain | ||||||
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![]() | PROTEIN TRANSPORT/HYDROLASE / PROTEIN-PROTEIN INTERACTION / PROTEIN TRANSPORT / BACTERIOCIN TRANSPORT / TOLB / COLICIN / PLASMID / NUCLEASE / HYDROLASE / TRANSPORT / ANTIBIOTIC / PERIPLASMIC / BACTERIOCIN / NATIVELY DISORDERED PROTEINS / PROTEIN TRANSPORT-HYDROLASE COMPLEX / ENDONUCLEASE / ANTIMICROBIAL / TRANSLOCATION | ||||||
Function / homology | ![]() cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / extrachromosomal circular DNA / protein import / cell division site / protein transport / outer membrane-bounded periplasmic space / endonuclease activity / killing of cells of another organism ...cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / extrachromosomal circular DNA / protein import / cell division site / protein transport / outer membrane-bounded periplasmic space / endonuclease activity / killing of cells of another organism / periplasmic space / Hydrolases; Acting on ester bonds / defense response to bacterium / cell cycle / protein domain specific binding / cell division / protein-containing complex binding / protein-containing complex / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Loftus, S.R. / Walker, D. / Mate, M.J. / Bonsor, D.A. / James, R. / Moore, G.R. / Kleanthous, C. | ||||||
![]() | ![]() Title: Competitive Recruitment of the Periplasmic Translocation Portal Tolb by a Natively Disordered Domain of Colicin E9 Authors: Loftus, S.R. / Walker, D. / Mate, M.J. / Bonsor, D.A. / James, R. / Moore, G.R. / Kleanthous, C. #1: ![]() Title: Structure of the Escherichia Coli Tolb Protein Determined by MAD Methods at 1.95 A Resolution Authors: Abergel, C. / Bouveret, E. / Claverie, J.-M. / Brown, K. / Rigal, A. / Lazdunski, C. / Benedetti, H. #2: ![]() Title: The Structure of Tolb, an Essential Component of the Tol-Dependent Translocation System, and its Protein-Protein Interaction with the Translocation Domain of Colicin E9. Authors: Carr, S. / Penfold, C.N. / Bamford, V. / James, R. / Hemmings, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.8 KB | Display | ![]() |
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PDB format | ![]() | 274.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 476.5 KB | Display | ![]() |
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Full document | ![]() | 489 KB | Display | |
Data in XML | ![]() | 68.3 KB | Display | |
Data in CIF | ![]() | 101.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c5kS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47196.594 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1607.553 Da / Num. of mol.: 4 / Fragment: T-DOMAIN, RESIDUES 32-47 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() References: UniProt: P09883, Hydrolases; Acting on ester bonds #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Compound details | PARTICIPATES IN THE UPTAKE OF GROUP A COLOCINS IN A TONB INDEPENDENT MANNER.THE PEPTIDE WHICH COMES ...PARTICIPAT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | pH: 7.5 Details: 24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→144 Å / Num. obs: 102162 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1C5K Resolution: 2→144.34 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.705 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.169 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2→144.34 Å
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