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Yorodumi- PDB-1ek9: 2.1A X-RAY STRUCTURE OF TOLC: AN INTEGRAL OUTER MEMBRANE PROTEIN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ek9 | ||||||
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Title | 2.1A X-RAY STRUCTURE OF TOLC: AN INTEGRAL OUTER MEMBRANE PROTEIN AND EFFLUX PUMP COMPONENT FROM ESCHERICHIA COLI | ||||||
Components | OUTER MEMBRANE PROTEIN TOLC | ||||||
Keywords | MEMBRANE PROTEIN / Integral membrane protein / Alpha helical Barrel / Beta 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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Koronakis, V. / Sharff, A.J. / Koronakis, E. / Luisi, B. / Hughes, C. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Crystal structure of the bacterial membrane protein TolC central to multidrug efflux and protein export. Authors: Koronakis, V. / Sharff, A. / Koronakis, E. / Luisi, B. / Hughes, C. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Oxidation of Selenomethionine: Some MADness in the Method! Authors: Sharff, A.J. / Koronakis, E. / Luisi, B. / Koronakis, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ek9.cif.gz | 282.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ek9.ent.gz | 236.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ek9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ek9_validation.pdf.gz | 441.3 KB | Display | wwPDB validaton report |
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Full document | 1ek9_full_validation.pdf.gz | 497.3 KB | Display | |
Data in XML | 1ek9_validation.xml.gz | 68.3 KB | Display | |
Data in CIF | 1ek9_validation.cif.gz | 101.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ek9 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ek9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a homo-trimer constructed from chains A, B and C |
-Components
#1: Protein | Mass: 47238.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PACYC184 / Production host: Escherichia coli (E. coli) / References: UniProt: P02930 #2: 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: 4.58 Å3/Da / Density % sol: 73.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 2000 MME, PEG 400, Sodium Chloride, Magnesium Chloride, dodecyl glucopyrsanoside, hexyl glucopyranoside, heptyl gluocopyranoside, octyl glucopyranoside, 1,2,3-heptanetriol, Tris, pH 7.4, ...Details: PEG 2000 MME, PEG 400, Sodium Chloride, Magnesium Chloride, dodecyl glucopyrsanoside, hexyl glucopyranoside, heptyl gluocopyranoside, octyl glucopyranoside, 1,2,3-heptanetriol, Tris, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→129 Å / Num. all: 146143 / Num. obs: 1388136 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.261 / Num. unique all: 15808 / % possible all: 99.6 |
Reflection | *PLUS Num. obs: 146143 / Num. measured all: 1388136 |
Reflection shell | *PLUS % possible obs: 99.6 % / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The coordinates deposited are of the selenomethione substituted protein. Methionine residues at positions 4, 78, 279, 297 and 358 have been replaced with selenomethionine.
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'BUSTER/TNT' / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.88 Å2 |