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- PDB-5iva: The LPS Transporter LptDE from Pseudomonas aeruginosa, core complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iva | ||||||
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Title | The LPS Transporter LptDE from Pseudomonas aeruginosa, core complex | ||||||
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![]() | TRANSPORT PROTEIN / LptD / LptE / lipopolysaccharide / Transporter | ||||||
Function / homology | ![]() regulation of polysaccharide biosynthetic process / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / : / lipopolysaccharide binding / cell outer membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Botos, I. / 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 | ![]() | 165.1 KB | Display | ![]() |
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PDB format | ![]() | 130.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 37.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5iv8C ![]() 5iv9C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 75433.367 Da / Num. of mol.: 1 / Fragment: unp residues 300-924 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 21316.590 Da / Num. of mol.: 1 / Fragment: unp residues 21-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.59 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM sodium citrate pH 5.5, 100 mM sodium chloride, 100 mM lithium chloride, 12% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.988→49.089 Å / Num. obs: 27493 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 12.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Q35 Resolution: 2.988→49.089 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.988→49.089 Å
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Refine LS restraints |
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LS refinement shell |
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