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- PDB-1sxr: Drosophila Peptidoglycan Recognition Protein (PGRP)-SA -

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Basic information

Entry
Database: PDB / ID: 1sxr
TitleDrosophila Peptidoglycan Recognition Protein (PGRP)-SA
ComponentsPeptidoglycan recognition protein SA CG11709-PA
KeywordsIMMUNE SYSTEM / Pattern Recognition Receptor / peptidoglycan / innate immunity / Toll pathway
Function / homology
Function and homology information


Toll receptor ligand protein activation cascade / Antimicrobial peptides / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / peptidoglycan immune receptor activity / response to peptidoglycan / Neutrophil degranulation / peptidoglycan binding ...Toll receptor ligand protein activation cascade / Antimicrobial peptides / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / peptidoglycan immune receptor activity / response to peptidoglycan / Neutrophil degranulation / peptidoglycan binding / pattern recognition receptor activity / peptidoglycan catabolic process / defense response to Gram-positive bacterium / innate immune response / proteolysis / 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
Peptidoglycan-recognition protein SA
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsReiser, J.B. / Teyton, L. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the Drosophila peptidoglycan recognition protein (PGRP)-SA at 1.56 A resolution
Authors: Reiser, J.B. / Teyton, L. / Wilson, I.A.
#1: Journal: Mol.Immunol. / Year: 2003
Title: CRYSTAL STRUCTURE OF PEPTIDOGLYCAN RECOGNITION PROTEIN LB FROM DROSOPHILA MELANOGASTER
Authors: Kim, M.S. / Byun, M. / Oh, B.H.
History
DepositionMar 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan recognition protein SA CG11709-PA
B: Peptidoglycan recognition protein SA CG11709-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0328
Polymers40,5922
Non-polymers4406
Water6,990388
1
A: Peptidoglycan recognition protein SA CG11709-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5785
Polymers20,2961
Non-polymers2824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Peptidoglycan recognition protein SA CG11709-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4543
Polymers20,2961
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Peptidoglycan recognition protein SA CG11709-PA
hetero molecules

B: Peptidoglycan recognition protein SA CG11709-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0328
Polymers40,5922
Non-polymers4406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area1980 Å2
ΔGint-42 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.29, 64.42, 45.87
Angle α, β, γ (deg.)90.00, 100.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-451-

HOH

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Components

#1: Protein Peptidoglycan recognition protein SA CG11709-PA


Mass: 20295.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pRMHa3 / Cell (production host): SC2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9VYX7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.55 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.3 to 1.5 M Li2SO4 and 0.1 M MES , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.069 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.069 Å / Relative weight: 1
ReflectionResolution: 1.56→45.13 Å / Num. all: 54845 / Num. obs: 54845 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 10.7
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2 / Num. unique all: 5148 / Rsym value: 0.451 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OHT

1oht


Resolution: 1.56→45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.427 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: Engh & Huber / Details: SSBOND were refined as partially reduced
RfactorNum. reflection% reflectionSelection details
Rfree0.211 5275 10.1 %RANDOM
Rwork0.177 ---
all0.181 52381 --
obs0.181 52381 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å2-0.52 Å2
2---0.71 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.56→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 26 388 3128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212848
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.9193870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8015344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26724.638138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73415448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.726158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022192
X-RAY DIFFRACTIONr_nbd_refined0.220.31285
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5489
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.536
X-RAY DIFFRACTIONr_mcbond_it0.9281.51752
X-RAY DIFFRACTIONr_mcangle_it1.38722750
X-RAY DIFFRACTIONr_scbond_it2.32431261
X-RAY DIFFRACTIONr_scangle_it3.0344.51120
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.29 317
Rwork0.233 2635
obs-2952

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