+Open data
-Basic information
Entry | Database: PDB / ID: 2w8b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of processed TolB in complex with Pal | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT/MEMBRANE PROTEIN / PROTEIN TRANSPORT MEMBRANE PROTEIN COMPLEX / TOL / PAL / TOLB / MEMBRANE / PALMITATE / PERIPLASM / BACTERIOCIN TRANSPORT / TRANSPORT PROTEIN/LIPOPROTEIN / CELL OUTER MEMBRANE / TRANSPORT / LIPOPROTEIN / CELL MEMBRANE / OUTER MEMBRANE / PROTEIN TRANSPORT-MEMBRANE PROTEIN complex | ||||||
Function / homology | Function and homology information cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / cell outer membrane / protein transport / outer membrane-bounded periplasmic space / periplasmic space / protein domain specific binding ...cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / cell outer membrane / protein transport / outer membrane-bounded periplasmic space / periplasmic space / protein domain specific binding / cell division / protein-containing complex binding / protein-containing complex / membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Sharma, A. / Bonsor, D.A. / Kleanthous, C. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Allosteric Beta-Propeller Signalling in Tolb and its Manipulation by Translocating Colicins. Authors: Bonsor, D.A. / Hecht, O. / Vankemmelbeke, M. / Sharma, A. / Krachler, A.M. / Housden, N.G. / Lilly, K.J. / James, R. / Moore, G.R. / Kleanthous, C. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2w8b.cif.gz | 429.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w8b.ent.gz | 349.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w8b_validation.pdf.gz | 534 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2w8b_full_validation.pdf.gz | 584.3 KB | Display | |
Data in XML | 2w8b_validation.xml.gz | 93.6 KB | Display | |
Data in CIF | 2w8b_validation.cif.gz | 136.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/2w8b ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w8b | HTTPS FTP |
-Related structure data
Related structure data | 2hqsS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 8 molecules ABDFCEGH
#1: Protein | Mass: 43637.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A855 | ||
---|---|---|---|
#2: Protein | Mass: 43637.379 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A855 #3: Protein | Mass: 13518.095 Da / Num. of mol.: 4 / Fragment: RESIDUES 65-173 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A912 |
-Non-polymers , 4 types, 1538 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-ACT / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % / Description: NONE |
---|---|
Crystal grow | pH: 4.6 Details: 0.1M SODIUM ACETATE PH 4.6, 17% PEG4000, 0.2M AMMONIUM SULPHATE, 20MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→45.74 Å / Num. obs: 176410 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.2 / % possible all: 94.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2HQS Resolution: 1.86→45.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.693 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.79 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→45.36 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|