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

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Basic information

Entry
Database: PDB / ID: 7xfy
TitleCrystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.67 A resolution.
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / CPGRP-S / PGRP-S / Peptidoglycan 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 / ACETATE ION / L(+)-TARTARIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsMaurya, A. / Singh, P.K. / Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.67 A resolution.
Authors: Maurya, A. / Singh, P.K. / Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionApr 2, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 11, 2022ID: 6JX8
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 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

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)77,17117
Polymers76,0464
Non-polymers1,12513
Water6,287349
1
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3957
Polymers38,0232
Non-polymers3725
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)89.583, 101.026, 163.412
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-317-

HOH

21C-350-

HOH

31D-341-

HOH

41D-388-

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, 362 molecules

#2: 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
#3: 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
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / 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.: 349 / 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: 2.43 Å3/Da / Density % sol: 49.5 %
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: 0.966 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: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.67→85.93 Å / Num. obs: 19639 / % possible obs: 91.49 % / Redundancy: 4.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.06 / Net I/σ(I): 12.6
Reflection shellResolution: 2.67→2.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.718 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1087 / CC1/2: 0.776 / Rpim(I) all: 0.367 / % possible all: 90

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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: 2.67→85.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.872 / SU B: 15.846 / SU ML: 0.309 / Cross valid method: FREE R-VALUE / ESU R Free: 0.408
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2657 961 4.893 %
Rwork0.1754 18678 -
all0.18 --
obs-19639 91.502 %
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: 33.021 Å2
Baniso -1Baniso -2Baniso -3
1--0.176 Å2-0 Å20 Å2
2--0.169 Å2-0 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 2.67→85.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 73 349 5625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174840
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6537361
X-RAY DIFFRACTIONr_angle_other_deg1.2641.57211150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7885660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44819.506324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93615804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9281564
X-RAY DIFFRACTIONr_chiral_restr0.0720.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026204
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021276
X-RAY DIFFRACTIONr_nbd_refined0.2030.21196
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.25050
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22596
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22520
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0410.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.218
X-RAY DIFFRACTIONr_nbd_other0.20.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.26
X-RAY DIFFRACTIONr_mcbond_it3.0533.3682655
X-RAY DIFFRACTIONr_mcbond_other3.0493.3672654
X-RAY DIFFRACTIONr_mcangle_it4.7865.033309
X-RAY DIFFRACTIONr_mcangle_other4.7865.0323310
X-RAY DIFFRACTIONr_scbond_it3.5923.762760
X-RAY DIFFRACTIONr_scbond_other3.5913.762761
X-RAY DIFFRACTIONr_scangle_it5.6315.4864052
X-RAY DIFFRACTIONr_scangle_other5.635.4874053
X-RAY DIFFRACTIONr_lrange_it10.03363.66425067
X-RAY DIFFRACTIONr_lrange_other10.03363.66225066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.7390.405660.3481087X-RAY DIFFRACTION74.1479
2.739-2.8140.359570.2911097X-RAY DIFFRACTION75.8213
2.814-2.8960.358490.2361113X-RAY DIFFRACTION78.4605
2.896-2.9850.311540.2211112X-RAY DIFFRACTION81.0848
2.985-3.0820.312550.2121119X-RAY DIFFRACTION84.0974
3.082-3.190.302690.211143X-RAY DIFFRACTION89.7113
3.19-3.3110.346560.2031240X-RAY DIFFRACTION97.3704
3.311-3.4460.284560.1841186X-RAY DIFFRACTION99.5192
3.446-3.5990.281560.1741150X-RAY DIFFRACTION99.6694
3.599-3.7740.219660.1571098X-RAY DIFFRACTION99.4872
3.774-3.9780.238580.1481032X-RAY DIFFRACTION99.4526
3.978-4.2180.28530.1481007X-RAY DIFFRACTION99.7178
4.218-4.5090.202510.139929X-RAY DIFFRACTION99.4924
4.509-4.8690.21520.137864X-RAY DIFFRACTION99.5652
4.869-5.3320.274440.16817X-RAY DIFFRACTION99.5376
5.332-5.9590.31370.157738X-RAY DIFFRACTION99.6144
5.959-6.8750.301290.153661X-RAY DIFFRACTION98.9957
6.875-8.4060.192240.13565X-RAY DIFFRACTION99.6616
8-100.114100.114270X-RAY DIFFRACTION95.8904
8.406-11.8320.135190.113450X-RAY DIFFRACTION98.9451

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