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- PDB-2eax: Crystal structure of human PGRP-IBETAC in complex with glycosamyl... -

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Basic information

Entry
Database: PDB / ID: 2eax
TitleCrystal structure of human PGRP-IBETAC in complex with glycosamyl muramyl pentapeptide
Components
  • GLYCOSAMYL MURAMYL PENTAPEPTIDE
  • Peptidoglycan recognition protein-I-beta
KeywordsPEPTIDOGLYCAN-BINDING PROTEIN / ALPHA/BETA
Function / homology
Function and homology information


peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / Antimicrobial peptides / detection of bacterium / peptidoglycan catabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to Gram-positive bacterium / protein heterodimerization activity ...peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / Antimicrobial peptides / detection of bacterium / peptidoglycan catabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to Gram-positive bacterium / protein heterodimerization activity / innate immune response / protein-containing complex / zinc ion binding / extracellular region / 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 / Ami_2 / 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 4 / Peptidoglycan recognition protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCho, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins
Authors: Cho, S. / Wang, Q. / Swaminathan, C.P. / Hesek, D. / Lee, M. / Boons, G.J. / Mobashery, S. / Mariuzza, R.A.
History
DepositionFeb 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Sep 14, 2011Group: Non-polymer description
Revision 1.4Sep 21, 2011Group: Source and taxonomy / Structure summary
Revision 1.5Dec 17, 2014Group: Atomic model / Derived calculations
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan recognition protein-I-beta
B: Peptidoglycan recognition protein-I-beta
C: Peptidoglycan recognition protein-I-beta
L: GLYCOSAMYL MURAMYL PENTAPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7675
Polymers54,2574
Non-polymers5101
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.940, 61.390, 97.950
Angle α, β, γ (deg.)90.00, 96.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidoglycan recognition protein-I-beta


Mass: 17922.479 Da / Num. of mol.: 3 / Fragment: peptidoglycan-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGRPIB / Plasmid: PT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q3B822, UniProt: Q96LB8*PLUS
#2: Protein/peptide GLYCOSAMYL MURAMYL PENTAPEPTIDE


Mass: 489.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The sequence of the peptide is naturally in human. / Source: (synth.) Homo sapiens (human)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 510.490 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC_2*NCC/3=O_3*OC^RCO/4=O/3C][a2122h-1b_1-5_2*NCC/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][<C3O1>]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ENTIRE CHAIN L (RESIDUES 500-506) IS GLYCOSAMYL MURAMYL PENTAPEPTIDE. THE SEQUENCE IS NAG AMV ...THE ENTIRE CHAIN L (RESIDUES 500-506) IS GLYCOSAMYL MURAMYL PENTAPEPTIDE. THE SEQUENCE IS NAG AMV ALA FGA LYS DAL DAL.

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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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% (v/v) Tacsimate, 0.1M Hepes pH 7.0, 2% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2006 / Details: mirror
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 27838 / Num. obs: 27509 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.273 / Num. unique all: 1328 / % possible all: 96.72

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EAV

2eav


Resolution: 2.1→30 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 670 -RANDOM
Rwork0.21 ---
all0.218 27838 --
obs0.215 27509 97.92 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 34 320 4165
LS refinement shellResolution: 2.1→2.16 Å
RfactorNum. reflection% reflection
Rfree0.341 --
Rwork0.307 --
obs-1328 96.72 %

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