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- PDB-1z6i: Crystal structure of the ectodomain of Drosophila transmembrane r... -

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Basic information

Entry
Database: PDB / ID: 1z6i
TitleCrystal structure of the ectodomain of Drosophila transmembrane receptor PGRP-LCa
ComponentsPeptidoglycan-recognition protein-LC
KeywordsMEMBRANE PROTEIN / IMMUNE SYSTEM / MIXED BETA-SHEET / 3/10 helix
Function / homology
Function and homology information


regulation of melanization defense response / Peptidoglycans (PGN) bind to a peptidoglycan recognition protein receptor, PGRP-LC/LE / Peptidoglycan bound PGRP-LC/LE oligomerises / Assembly of the PGN:PGRP-LC/LE receptor 'signalling complex' / Activated IkappaB kinase (IKK) complex, Phospho IRD5:KEY dimer, phosphorylates REL in the PGN:PGRP-LC/LE receptor 'signalling complex' / REL binds to DREDD in the PGN:PGRP-LC/LE receptor 'signalling complex' / Phosphorylated REL is cleaved by and dissociates from DREDD / peptidoglycan recognition protein signaling pathway / positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / positive regulation of antibacterial peptide biosynthetic process ...regulation of melanization defense response / Peptidoglycans (PGN) bind to a peptidoglycan recognition protein receptor, PGRP-LC/LE / Peptidoglycan bound PGRP-LC/LE oligomerises / Assembly of the PGN:PGRP-LC/LE receptor 'signalling complex' / Activated IkappaB kinase (IKK) complex, Phospho IRD5:KEY dimer, phosphorylates REL in the PGN:PGRP-LC/LE receptor 'signalling complex' / REL binds to DREDD in the PGN:PGRP-LC/LE receptor 'signalling complex' / Phosphorylated REL is cleaved by and dissociates from DREDD / peptidoglycan recognition protein signaling pathway / positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria / positive regulation of antibacterial peptide biosynthetic process / regulation of humoral immune response / lipopolysaccharide immune receptor activity / peptidoglycan immune receptor activity / apicolateral plasma membrane / peptidoglycan binding / detection of bacterium / response to bacterium / regulation of synaptic plasticity / presynapse / antibacterial humoral response / cytoplasmic vesicle / defense response to Gram-negative bacterium / defense response to virus / defense response to Gram-positive bacterium / immune response / innate immune response / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Lysozyme-like / Peptidoglycan recognition protein-like / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan-recognition protein LC
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChang, C.-I. / Ihara, K. / Chelliah, Y. / Mengin-Lecreulx, D. / Wakatsuki, S. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of the ectodomain of Drosophila peptidoglycan-recognition protein LCa suggests a molecular mechanism for pattern recognition
Authors: Chang, C.-I. / Ihara, K. / Chelliah, Y. / Mengin-Lecreulx, D. / Wakatsuki, S. / Deisenhofer, J.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan-recognition protein-LC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1154
Polymers18,7011
Non-polymers4133
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.799, 105.799, 105.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Peptidoglycan-recognition protein-LC / Immune response deficient 7 protein


Mass: 18701.281 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PGRP-LC, ird7, PGRPLC / Plasmid: pFASTBAC-HTa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9GNK5
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: ammonium sulphate, phosphate citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2005
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→74.54 Å / Num. all: 7484 / Num. obs: 7439 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.44
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.42 / Num. unique all: 719 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→74.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 405 5.5 %RANDOM
Rwork0.213 ---
all0.225 7439 --
obs0.215 7002 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.742 Å2
Refinement stepCycle: LAST / Resolution: 2.5→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 24 25 1365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211371
X-RAY DIFFRACTIONr_bond_other_d0.0020.021215
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9631864
X-RAY DIFFRACTIONr_angle_other_deg0.80332829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021498
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02273
X-RAY DIFFRACTIONr_nbd_refined0.1940.2252
X-RAY DIFFRACTIONr_nbd_other0.2340.21375
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.5832
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08221342
X-RAY DIFFRACTIONr_scbond_it1.4833539
X-RAY DIFFRACTIONr_scangle_it2.6664.5522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.566 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.396 29
Rwork0.25 505

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