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- PDB-7xfw: Crystal structure of the ternary complex of Peptidoglycan recogni... -

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Basic information

Entry
Database: PDB / ID: 7xfw
TitleCrystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.07 A resolution.
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / CPGRP-S / PGRP-S
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. / 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 / ACETATE ION / L(+)-TARTARIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsMaurya, A. / Singh, P.K. / Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2022
Title: Structure of the complex of camel peptidoglycan recognition protein-S with hexanoic acid reveals novel features of the versatile ligand-binding site at the dimeric interface.
Authors: Maurya, A. / Sharma, P. / Singh, P.K. / Viswanathan, V. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 2, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 11, 2022ID: 6J3W
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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

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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)77,28919
Polymers76,0464
Non-polymers1,24415
Water8,413467
1
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5139
Polymers38,0232
Non-polymers4907
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)38,77710
Polymers38,0232
Non-polymers7548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.889, 101.508, 162.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-341-

HOH

21C-362-

HOH

31D-319-

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 , 7 types, 482 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.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 48.51 %
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: MASSIF-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 7, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.07→46.36 Å / Num. obs: 45175 / % possible obs: 99.82 % / Redundancy: 6.94 % / CC1/2: 0.99 / Rpim(I) all: 0.041 / Net I/σ(I): 8.13
Reflection shellResolution: 2.07→2.12 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1297 / CC1/2: 0.869 / Rpim(I) all: 0.433 / % possible all: 99.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DWF

5dwf


Resolution: 2.07→46.358 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.577 / SU ML: 0.188 / Cross valid method: FREE R-VALUE / ESU R: 0.22 / ESU R Free: 0.195
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2576 1297 2.871 %
Rwork0.1998 43877 -
all0.202 --
obs-45174 99.817 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.018 Å20 Å20 Å2
2---0.021 Å20 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 2.07→46.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 81 467 5751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135428
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174850
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6537377
X-RAY DIFFRACTIONr_angle_other_deg1.3511.57211172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.395660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47919.508325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16515805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.041564
X-RAY DIFFRACTIONr_chiral_restr0.0750.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021278
X-RAY DIFFRACTIONr_nbd_refined0.1990.21198
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.25039
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22653
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2360
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.214
X-RAY DIFFRACTIONr_nbd_other0.1880.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.210
X-RAY DIFFRACTIONr_mcbond_it2.713.6762657
X-RAY DIFFRACTIONr_mcbond_other2.7093.6752656
X-RAY DIFFRACTIONr_mcangle_it3.8785.4953309
X-RAY DIFFRACTIONr_mcangle_other3.8775.4963310
X-RAY DIFFRACTIONr_scbond_it3.1574.0642771
X-RAY DIFFRACTIONr_scbond_other3.1564.0642772
X-RAY DIFFRACTIONr_scangle_it4.8775.954068
X-RAY DIFFRACTIONr_scangle_other4.8775.954069
X-RAY DIFFRACTIONr_lrange_it6.7444.1996351
X-RAY DIFFRACTIONr_lrange_other6.73844.1996351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.1230.394940.3563173X-RAY DIFFRACTION99.7862
2.123-2.1820.351920.3313129X-RAY DIFFRACTION100
2.182-2.2450.374900.3173050X-RAY DIFFRACTION99.9045
2.245-2.3140.348870.2852938X-RAY DIFFRACTION99.7034
2.314-2.3890.325850.2622860X-RAY DIFFRACTION100
2.389-2.4730.306820.2492786X-RAY DIFFRACTION99.9651
2.473-2.5660.316790.2232689X-RAY DIFFRACTION100
2.566-2.670.352770.2392582X-RAY DIFFRACTION99.6253
2.67-2.7890.383730.2542496X-RAY DIFFRACTION99.8834
2.789-2.9240.356700.2332360X-RAY DIFFRACTION100
2.924-3.0820.223670.1962264X-RAY DIFFRACTION100
3.082-3.2680.248640.182144X-RAY DIFFRACTION99.9547
3.268-3.4920.209590.1742026X-RAY DIFFRACTION99.5227
3.492-3.770.175560.161893X-RAY DIFFRACTION99.7952
3.77-4.1270.241510.1571723X-RAY DIFFRACTION99.3281
4.127-4.610.196470.1441601X-RAY DIFFRACTION99.8788
4.61-5.3140.196420.1541409X-RAY DIFFRACTION99.3155
5.314-6.4870.248360.1741198X-RAY DIFFRACTION99.8382
6.487-9.0860.177280.149970X-RAY DIFFRACTION100
8-100.212180.162586X-RAY DIFFRACTION99.67

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