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- PDB-5iv8: The LPS Transporter LptDE from Klebsiella pneumoniae, core complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iv8 | ||||||
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Title | The LPS Transporter LptDE from Klebsiella pneumoniae, core complex | ||||||
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![]() | TRANSPORT PROTEIN / LptD / LptE / lipopolysaccharide / Transporter | ||||||
Function / homology | ![]() lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / : / cell outer membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Botos, I. / McCarthy, J.G. / Buchanan, S.K. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens. Authors: Botos, I. / Majdalani, N. / Mayclin, S.J. / McCarthy, J.G. / Lundquist, K. / Wojtowicz, D. / Barnard, T.J. / Gumbart, J.C. / Buchanan, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 569.3 KB | Display | ![]() |
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PDB format | ![]() | 470.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 49.4 KB | Display | |
Data in CIF | ![]() | 65.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5iv9C ![]() 5ivaC ![]() 5ixmC ![]() 4q35S C: citing same article ( 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 69113.391 Da / Num. of mol.: 2 / Fragment: unp residues 203-782 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 19863.355 Da / Num. of mol.: 2 / Fragment: unp residues 20-196 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.31 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% PEG4K, 200mM ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.938→46.58 Å / Num. obs: 41834 / % possible obs: 97.4 % / Redundancy: 4 % / Net I/σ(I): 16.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Q35 Resolution: 2.938→41.414 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.938→41.414 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.6673 Å / Origin y: -56.9339 Å / Origin z: -64.1474 Å
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Refinement TLS group | Selection details: all |