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- PDB-5nur: Structural basis for maintenance of bacterial outer membrane lipi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nur | |||||||||
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Title | Structural basis for maintenance of bacterial outer membrane lipid asymmetry | |||||||||
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![]() | MEMBRANE PROTEIN / Outer membrane / lipid asymmetry / lipoprotein / phospholipid translocation | |||||||||
Function / homology | ![]() intermembrane phospholipid transfer / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding ...intermembrane phospholipid transfer / colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion channel activity / lipid binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Authors: Abellon-Ruiz, J. / Kaptan, S.S. / Basle, A. / Claudi, B. / Bumann, D. / Kleinekathofer, U. / van den Berg, B. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 646.4 KB | Display | ![]() |
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PDB format | ![]() | 545.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5nuoC ![]() 5nupC ![]() 5nuqC ![]() 2zfgS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 2 types, 6 molecules CAEDBF
#1: Protein | Mass: 37114.250 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ompF, cmlB, coa, cry, tolF, b0929, JW0912 / Production host: ![]() ![]() #2: Protein | Mass: 26364.527 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: mlaA, vacJ, AGG09_21815, BB749_07690, BCB67_11070, BL143_09030, BN49_3944, PMK1_00224, SAMEA3531778_01593, SM30_03044, SM57_02930 Production host: ![]() ![]() |
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-Sugars , 3 types, 3 molecules
#3: Polysaccharide | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose Type: oligosaccharide / Mass: 720.464 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 14 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/C8E.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/C8E.gif)
#6: Chemical | #7: Chemical | ChemComp-SO4 / #8: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.36 Å3/Da / Density % sol: 77.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.05 M sodium sulfate, 0.05 M lithium sulfate, 0.05 M Tris pH 8.5 and 35 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97956 Å / Relative weight: 1 |
Reflection | Resolution: 3.29→54.27 Å / Num. obs: 60533 / % possible obs: 99.4 % / Redundancy: 3.9 % / CC1/2: 0.98 / Rpim(I) all: 0.095 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.29→3.35 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3023 / CC1/2: 0.743 / Rpim(I) all: 0.534 / % possible all: 99.1 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2ZFG Resolution: 3.29→47.399 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.16
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.29→47.399 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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