+Open data
-Basic information
Entry | Database: PDB / ID: 4m4d | ||||||
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Title | Crystal structure of lipopolysaccharide binding protein | ||||||
Components | Lipopolysaccharide-binding protein | ||||||
Keywords | LIPID BINDING PROTEIN / beta barrel / immune response / lipopolysaccharide / blood | ||||||
Function / homology | Function and homology information positive regulation of cytolysis / Transfer of LPS from LBP carrier to CD14 / positive regulation of tumor necrosis factor production => GO:0032760 / macromolecule localization / Toll Like Receptor 4 (TLR4) Cascade / Regulation of TLR by endogenous ligand / detection of molecule of bacterial origin / lipoteichoic acid binding / leukocyte chemotaxis involved in inflammatory response / opsonization ...positive regulation of cytolysis / Transfer of LPS from LBP carrier to CD14 / positive regulation of tumor necrosis factor production => GO:0032760 / macromolecule localization / Toll Like Receptor 4 (TLR4) Cascade / Regulation of TLR by endogenous ligand / detection of molecule of bacterial origin / lipoteichoic acid binding / leukocyte chemotaxis involved in inflammatory response / opsonization / positive regulation of toll-like receptor 4 signaling pathway / regulation of membrane permeability / lipopolysaccharide transport / positive regulation of phagocytosis, engulfment / lipopeptide binding / positive regulation of respiratory burst involved in inflammatory response / macrophage activation involved in immune response / positive regulation of macrophage activation / positive regulation of neutrophil chemotaxis / cellular response to lipoteichoic acid / negative regulation of tumor necrosis factor production / positive regulation of chemokine production / lipopolysaccharide-mediated signaling pathway / acute-phase response / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / response to lipopolysaccharide / defense response to Gram-positive bacterium / innate immune response / signaling receptor binding / cell surface / extracellular space / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 Å | ||||||
Authors | Eckert, J.K. / Kim, Y.J. / Kim, J.I. / Gurtler, K. / Oh, D.Y. / Ploeg, A.H. / Pickkers, P. / Lundvall, L. / Hamann, L. / Giamarellos-Bourboulis, E. ...Eckert, J.K. / Kim, Y.J. / Kim, J.I. / Gurtler, K. / Oh, D.Y. / Ploeg, A.H. / Pickkers, P. / Lundvall, L. / Hamann, L. / Giamarellos-Bourboulis, E. / Kubarenko, A.V. / Weber, A.N. / Kabesch, M. / Kumpf, O. / An, H.J. / Lee, J.O. / Schumann, R.R. | ||||||
Citation | Journal: Immunity / Year: 2013 Title: The crystal structure of lipopolysaccharide binding protein reveals the location of a frequent mutation that impairs innate immunity. Authors: Eckert, J.K. / Kim, Y.J. / Kim, J.I. / Gurtler, K. / Oh, D.Y. / Sur, S. / Lundvall, L. / Hamann, L. / van der Ploeg, A. / Pickkers, P. / Giamarellos-Bourboulis, E. / Kubarenko, A.V. / Weber, ...Authors: Eckert, J.K. / Kim, Y.J. / Kim, J.I. / Gurtler, K. / Oh, D.Y. / Sur, S. / Lundvall, L. / Hamann, L. / van der Ploeg, A. / Pickkers, P. / Giamarellos-Bourboulis, E. / Kubarenko, A.V. / Weber, A.N. / Kabesch, M. / Kumpf, O. / An, H.J. / Lee, J.O. / Schumann, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m4d.cif.gz | 192 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m4d.ent.gz | 152.6 KB | Display | PDB format |
PDBx/mmJSON format | 4m4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m4d_validation.pdf.gz | 887.2 KB | Display | wwPDB validaton report |
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Full document | 4m4d_full_validation.pdf.gz | 919.3 KB | Display | |
Data in XML | 4m4d_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 4m4d_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/4m4d ftp://data.pdbj.org/pub/pdb/validation_reports/m4/4m4d | HTTPS FTP |
-Related structure data
Related structure data | 1ewfS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 51806.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lbp / Plasmid: pVL1393 / Cell line (production host): Hi-Five / Production host: Escherichia coli (E. coli) / References: UniProt: Q61805 #2: Sugar | ChemComp-NAG / #3: Chemical | |
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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: 2.61 Å3/Da / Density % sol: 52.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% PEG 8000, 100mM MOPS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.00599 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00599 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 22868 / Num. obs: 21741 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 73.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3.29 / Num. unique all: 2094 / Rsym value: 0.272 / % possible all: 76.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EWF Resolution: 2.909→19.891 Å / SU ML: 0.41 / σ(F): 1.34 / σ(I): 0 / Phase error: 34.34 / 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: 2.909→19.891 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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