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- PDB-4m4d: Crystal structure of lipopolysaccharide binding protein -

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Basic information

Entry
Database: PDB / ID: 4m4d
TitleCrystal structure of lipopolysaccharide binding protein
ComponentsLipopolysaccharide-binding proteinLipopolysaccharide binding protein
KeywordsLIPID 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 / lipoteichoic acid binding / detection of molecule of bacterial origin / 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 / lipoteichoic acid binding / detection of molecule of bacterial origin / leukocyte chemotaxis involved in inflammatory response / opsonization / lipopolysaccharide transport / positive regulation of toll-like receptor 4 signaling pathway / regulation of membrane permeability / 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 / positive regulation of interleukin-8 production / acute-phase response / 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 / signaling receptor binding / innate immune response / cell surface / extracellular space / membrane
Similarity search - Function
Lipopolysaccharide-binding protein / Lipid binding protein BPI/LBP / Bactericidal permeability-increasing protein; domain 2 / Bactericidal permeability-increasing protein; domain 2 / Lipid-binding serum glycoprotein, C-terminal / Lipid-binding serum glycoprotein, conserved site / LBP / BPI / CETP family, C-terminal domain / LBP / BPI / CETP family signature. / BPI/LBP/CETP N-terminal domain / BPI/LBP/CETP C-terminal domain ...Lipopolysaccharide-binding protein / Lipid binding protein BPI/LBP / Bactericidal permeability-increasing protein; domain 2 / Bactericidal permeability-increasing protein; domain 2 / Lipid-binding serum glycoprotein, C-terminal / Lipid-binding serum glycoprotein, conserved site / LBP / BPI / CETP family, C-terminal domain / LBP / BPI / CETP family signature. / BPI/LBP/CETP N-terminal domain / BPI/LBP/CETP C-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Lipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Lipopolysaccharide-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 Å
AuthorsEckert, 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.
CitationJournal: 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
DepositionAug 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide-binding protein
B: Lipopolysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,40614
Polymers103,6132
Non-polymers3,79212
Water0
1
A: Lipopolysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7037
Polymers51,8071
Non-polymers1,8966
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipopolysaccharide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7037
Polymers51,8071
Non-polymers1,8966
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.282, 59.906, 119.932
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipopolysaccharide-binding protein / Lipopolysaccharide binding protein / LBP


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 / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.00599 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00599 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EWF

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 1083 4.99 %RANDOM
Rwork0.2299 ---
all0.2322 21732 --
obs0.2322 21687 91.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.909→19.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6954 0 258 0 7212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127126
X-RAY DIFFRACTIONf_angle_d1.6719663
X-RAY DIFFRACTIONf_dihedral_angle_d17.6572652
X-RAY DIFFRACTIONf_chiral_restr0.0731108
X-RAY DIFFRACTIONf_plane_restr0.0111244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9088-3.04070.40791130.2832215077
3.0407-3.20040.36431300.2986249389
3.2004-3.40.32751400.2635264295
3.4-3.6610.33351410.2491272997
3.661-4.02660.29181440.222270796
4.0266-4.6030.23161430.1988273296
4.603-5.77570.24951380.2224260692
5.7757-19.8910.2421340.2205254587

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