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- PDB-3cxa: Crystal structure of the complex of peptidoglycan recognition pro... -

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Basic information

Entry
Database: PDB / ID: 3cxa
TitleCrystal structure of the complex of peptidoglycan recognition protein with alpha-D-glucopyranosyl alpha-D-glucopyranoside at 3.4 A resolution
ComponentsPeptidoglycan recognition protein
KeywordsANTIBIOTIC / Peptidoglycan recognition protein / complex / trehalose / immune response / secreted / antimicrobial / PGRP
Function / homology
Function and homology information


peptidoglycan immune receptor activity / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan binding / negative regulation of cytokine production / detection of bacterium / peptidoglycan catabolic process / defense response to Gram-positive bacterium / innate immune response / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan recognition protein, PGRP-S / 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 ...Peptidoglycan recognition protein, PGRP-S / 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
trehalose / L(+)-TARTARIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBalaji, K. / Sharma, P. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of peptidoglycan recognition protein with alpha-D-glucopyranosyl alpha-D-glucopyranoside at 3.4 A resolution
Authors: Balaji, K. / Sharma, P. / Singh, N. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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
B: Peptidoglycan recognition protein
C: Peptidoglycan recognition protein
D: Peptidoglycan recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8817
Polymers76,0464
Non-polymers8353
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peptidoglycan recognition protein
D: Peptidoglycan recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1733
Polymers38,0232
Non-polymers1501
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-13 kcal/mol
Surface area16430 Å2
MethodPISA
3
B: Peptidoglycan recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3542
Polymers19,0111
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: Peptidoglycan recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3542
Polymers19,0111
Non-polymers3421
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.640, 102.390, 163.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Peptidoglycan recognition protein / Peptidoglycan recognition protein short / PGRP-S


Mass: 19011.459 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Camelus dromedarius (Arabian camel) / Secretion: MILK / References: UniProt: Q9GK12
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6

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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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2M SODIUM POTASSIUM TARTRATE, 10% PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 2007 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→20 Å / Num. obs: 10724 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.5 Å2 / Rsym value: 0.182 / Net I/σ(I): 4.4
Reflection shellResolution: 3.4→3.52 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.545 / % possible all: 98.9

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Processing

Software
NameClassification
DENZOdata reduction
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2K

2r2k


Resolution: 3.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 551 -RANDOM
Rwork0.2252 ---
all0.2567 10473 --
obs0.2331 9922 93.2 %-
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 56 0 5400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d20

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