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- PDB-4rhb: Crystal structure of the lipopolysaccharide assembly complex LptD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rhb | ||||||
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Title | Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the Escherichia coli outer membrane | ||||||
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![]() | TRANSPORT PROTEIN / lipopolysaccharide assembly / lipid binding protein / outer membrane of Gram-negative bacteria / 26-stranded beta barrel and 2-layer beta sandwich | ||||||
Function / homology | ![]() lipopolysaccharide transport => GO:0015920 / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / : / lipopolysaccharide binding / cell outer membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malojcic, G. / Garner, R.A. / Kahne, D. | ||||||
![]() | ![]() Title: Structural basis of lipopolysaccharide insertion into the bacterial outer membrane Authors: Malojcic, G. / Garner, R.A. / Kahne, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.7 KB | Display | ![]() |
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PDB format | ![]() | 241 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
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Full document | ![]() | 510.3 KB | Display | |
Data in XML | ![]() | 50.9 KB | Display | |
Data in CIF | ![]() | 69.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rh8C ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 71233.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 19479.148 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % |
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.355→200 Å / Num. all: 27863 / Num. obs: 26835 / % possible obs: 96.3 % / Observed criterion σ(I): 0.47 |
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Processing
Software | Name: REFMAC / Version: 5.8.0071 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4Q35 Resolution: 3.355→108.31 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.864 / SU B: 57.935 / SU ML: 0.843 / Cross valid method: THROUGHOUT / ESU R Free: 0.786 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 115.877 Å2
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Refinement step | Cycle: LAST / Resolution: 3.355→108.31 Å
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Refine LS restraints |
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