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Open data
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Basic information
Entry | Database: PDB / ID: 5x5y | ||||||
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Title | A membrane protein complex | ||||||
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![]() | MEMBRANE PROTEIN / transporter | ||||||
Function / homology | ![]() lipopolysaccharide transport => GO:0015920 / lipopolysaccharide floppase activity / lipopolysaccharide transport / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Luo, Q. / Yang, X. / Huang, Y. | ||||||
![]() | ![]() Title: Structural basis for lipopolysaccharide extraction by ABC transporter LptB2FG Authors: Luo, Q. / Yang, X. / Yu, S. / Shi, H. / Wang, K. / Xiao, L. / Zhu, G. / Sun, C. / Li, T. / Li, D. / Zhang, X. / Zhou, M. / Huang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.5 KB | Display | ![]() |
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PDB format | ![]() | 190.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.7 KB | Display | ![]() |
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Full document | ![]() | 493.1 KB | Display | |
Data in XML | ![]() | 42.3 KB | Display | |
Data in CIF | ![]() | 57.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4qc2S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 240 / Label seq-ID: 2 - 240
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Components
#1: Protein | Mass: 27316.309 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 39235.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | | Mass: 40344.277 Da / Num. of mol.: 1 / Fragment: UNP residues 1-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.18 % |
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Crystal grow | Temperature: 277.15 K / Method: evaporation / pH: 7 / Details: PEG 2000, Hepes, magnesium chloride, HEGA-10 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.46→50 Å / Num. obs: 24569 / % possible obs: 99.4 % / Redundancy: 13.3 % / Biso Wilson estimate: 134.66 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.043 / Rrim(I) all: 0.159 / Χ2: 1.223 / Net I/σ(I): 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QC2 Resolution: 3.465→45.641 Å / SU ML: 0.52 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 37.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 237.98 Å2 / Biso mean: 145.7939 Å2 / Biso min: 58.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.465→45.641 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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