+Open data
-Basic information
Entry | Database: PDB / ID: 1tqq | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of TolC in complex with hexamminecobalt | ||||||
Components | Outer membrane protein tolC | ||||||
Keywords | TRANSPORT PROTEIN / Beta-barrel / alpha-barrel | ||||||
Function / homology | Function and homology information MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity ...MacAB-TolC complex / enterobactin transport / bile acid transmembrane transporter activity / xenobiotic detoxification by transmembrane export across the cell outer membrane / efflux pump complex / periplasmic side of plasma membrane / xenobiotic detoxification by transmembrane export across the plasma membrane / bile acid and bile salt transport / porin activity / efflux transmembrane transporter activity / monoatomic ion transmembrane transport / cell outer membrane / response to organic cyclic compound / response to toxic substance / monoatomic ion channel activity / outer membrane-bounded periplasmic space / response to xenobiotic stimulus / response to antibiotic / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Higgins, M.K. / Eswaran, J. / Edwards, P.C. / Schertler, G.F. / Hughes, C. / Koronakis, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structure of the ligand-blocked periplasmic entrance of the bacterial multidrug effllux protein TolC Authors: Higgins, M.K. / Eswaran, J. / Edwards, P.C. / Schertler, G.F. / Hughes, C. / Koronakis, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1tqq.cif.gz | 256.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1tqq.ent.gz | 208.8 KB | Display | PDB format |
PDBx/mmJSON format | 1tqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/1tqq ftp://data.pdbj.org/pub/pdb/validation_reports/tq/1tqq | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ek9S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 3 / Auth seq-ID: 1 - 428 / Label seq-ID: 1 - 428
|
-Components
#1: Protein | Mass: 51509.582 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TOLC, MTCB, MUKA, REFI, B3035 / Production host: Escherichia coli (E. coli) / References: UniProt: P02930 #2: Chemical | ChemComp-NCO / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.5 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% ...Details: 0.6% detergent mixture of n-dodecyl-beta-D glucopyranoside, n-hexyl-beta-D glucopyranoside, n-heptyl-beta-D glucopyranoside and n-octyl-beta-D glucopyranoside, 1.5% 1,2,3-heptanetriol, 7% polyethylene glycol 2000 monomethyl ether, 10% polyethylene glycol 400, 10mM NaCl, 20mM MgCl2, 20mM Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 2002 |
Radiation | Monochromator: Liquid gallium cooled, bent, triangular, si 111 optimised for: 1.2 (top crystal, 9.3 asymmetric cut) 1.488 (bottom crystal, 11.7 asymmetric cut) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→30 Å / Num. all: 65599 / Num. obs: 62730 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rsym value: 0.095 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.75→2.82 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2.1 / Num. unique all: 63790 / % possible all: 94.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1EK9 Resolution: 2.75→30.43 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.841 / SU B: 10.299 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 2 / ESU R: 0.555 / ESU R Free: 0.359 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.736 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→30.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.821 Å / Total num. of bins used: 20 /
|