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Yorodumi- PDB-6xlp: Structure of the essential inner membrane lipopolysaccharide-PbgA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xlp | ||||||
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Title | Structure of the essential inner membrane lipopolysaccharide-PbgA complex | ||||||
Components | LPS binding protein | ||||||
Keywords | LIPID BINDING PROTEIN / lipopolysaccharide / LPS / membrane protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Payandeh, J. / Clairefeuille, T. | ||||||
Citation | Journal: Nature / Year: 2020 Title: Structure of the essential inner membrane lipopolysaccharide-PbgA complex. Authors: Clairfeuille, T. / Buchholz, K.R. / Li, Q. / Verschueren, E. / Liu, P. / Sangaraju, D. / Park, S. / Noland, C.L. / Storek, K.M. / Nickerson, N.N. / Martin, L. / Dela Vega, T. / Miu, A. / ...Authors: Clairfeuille, T. / Buchholz, K.R. / Li, Q. / Verschueren, E. / Liu, P. / Sangaraju, D. / Park, S. / Noland, C.L. / Storek, K.M. / Nickerson, N.N. / Martin, L. / Dela Vega, T. / Miu, A. / Reeder, J. / Ruiz-Gonzalez, M. / Swem, D. / Han, G. / DePonte, D.P. / Hunter, M.S. / Gati, C. / Shahidi-Latham, S. / Xu, M. / Skelton, N. / Sellers, B.D. / Skippington, E. / Sandoval, W. / Hanan, E.J. / Payandeh, J. / Rutherford, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xlp.cif.gz | 266.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xlp.ent.gz | 210.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/6xlp ftp://data.pdbj.org/pub/pdb/validation_reports/xl/6xlp | HTTPS FTP |
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-Related structure data
Related structure data | 5i5hS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 68491.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yejM, pbgA, yejM_2 / Production host: Escherichia coli (E. coli) / References: UniProt: C3T3G2, UniProt: P0AD27*PLUS |
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#2: Polysaccharide | 2-deoxy-3-O-[(1R,3R)-1,3-dihydroxytetradecyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono- ...2-deoxy-3-O-[(1R,3R)-1,3-dihydroxytetradecyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose-(6-1)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)]1,5-anhydro-2-deoxy-2-{[(1S,3R)-1-hydroxy-3-(pentanoyloxy)undecyl]amino}-4-O-phosphono-D-glucitol Type: oligosaccharide / Mass: 1445.598 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 166 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-OLB / ( #5: Chemical | #6: Chemical | ChemComp-3PE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.59 % |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase / pH: 8 Details: LCP was formulated from monoolein (Sigma): phosphatidylethanolamine (E. coli PE, Avanti Polar Lipids) 99.5:0.5% m/m mixture at 40% hydration; crystallization solution contained 0.1 M Tris pH ...Details: LCP was formulated from monoolein (Sigma): phosphatidylethanolamine (E. coli PE, Avanti Polar Lipids) 99.5:0.5% m/m mixture at 40% hydration; crystallization solution contained 0.1 M Tris pH 8.0, 0.2 M ammonium sulfate, 40% PEG200 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.242 Å / Num. obs: 53215 / % possible obs: 88 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3926 / CC1/2: 0.741 / % possible all: 62.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I5H Resolution: 2→24.24 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.08 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138 Å2 / Biso mean: 51.56 Å2 / Biso min: 20.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→24.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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