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- PDB-7dy5: Structure of the ternary complex of peptidoglycan recognition pro... -

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Basic information

Entry
Database: PDB / ID: 7dy5
TitleStructure of the ternary complex of peptidoglycan recognition protein-short (PGRP-S) with hexanoic acid and tartaric acid at 2.30A resolution
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / Recognition protein
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 / extracellular region / zinc ion binding
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. / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
Similarity search - Domain/homology
HEXANOIC ACID / L(+)-TARTARIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaurya, A. / Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Structure of the ternary complex of peptidoglycan recognition protein-short (PGRP-S)
Authors: Maurya, A. / Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 17, 2021ID: 6JTE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1
C: Peptidoglycan recognition protein 1
D: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,08015
Polymers76,0464
Non-polymers1,03411
Water7,602422
1
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2715
Polymers38,0232
Non-polymers2483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Peptidoglycan recognition protein 1
D: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,81010
Polymers38,0232
Non-polymers7878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.085, 101.355, 163.022
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-336-

HOH

21C-395-

HOH

31D-326-

HOH

41D-350-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Peptidoglycan recognition protein 1 / 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) / References: UniProt: Q9GK12

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Non-polymers , 6 types, 433 molecules

#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 3350, 0.2M Sodium potassium tartrate, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 18, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→50.68 Å / Num. obs: 25883 / % possible obs: 78.01 % / Redundancy: 4.8 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.05 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1879 / CC1/2: 0.87 / Rpim(I) all: 0.32 / % possible all: 58

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J3W

6j3w
PDB Unreleased entry


Resolution: 2.3→50.68 Å / SU ML: 0.2923 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.0535
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 1313 5.07 %
Rwork0.1878 24565 -
obs0.191 25878 78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.25 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 67 422 5692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035406
X-RAY DIFFRACTIONf_angle_d0.65187345
X-RAY DIFFRACTIONf_chiral_restr0.0469763
X-RAY DIFFRACTIONf_plane_restr0.0038971
X-RAY DIFFRACTIONf_dihedral_angle_d15.9469772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.31521140.22371986X-RAY DIFFRACTION58.17
2.39-2.50.28281160.23342198X-RAY DIFFRACTION63.4
2.5-2.630.28511270.22612408X-RAY DIFFRACTION69.59
2.63-2.80.29581100.21432194X-RAY DIFFRACTION63.14
2.8-3.010.28351700.2152840X-RAY DIFFRACTION82.02
3.01-3.320.27531740.20173108X-RAY DIFFRACTION89.4
3.32-3.80.23981540.17662969X-RAY DIFFRACTION84.73
3.8-4.780.24131690.15443231X-RAY DIFFRACTION91.3
4.78-50.680.19271790.17323631X-RAY DIFFRACTION98.45

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