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

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Basic information

Entry
Database: PDB / ID: 7xfx
TitleCrystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 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: 2.28 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 2.28 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: 6JVE
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 20, 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)77,23018
Polymers76,0464
Non-polymers1,18414
Water7,350408
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)38,83611
Polymers38,0232
Non-polymers8139
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.661, 101.653, 163.328
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-337-

HOH

21C-399-

HOH

31D-333-

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, 422 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.42 Å3/Da / Density % sol: 49.46 %
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: 2.28→78.04 Å / Num. obs: 27481 / % possible obs: 80.68 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.05 / Net I/σ(I): 10.8
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1384 / CC1/2: 0.907 / Rpim(I) all: 0.35 / % possible all: 100

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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: 2.28→77.921 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.891 / SU B: 8.439 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.608 / ESU R Free: 0.296
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.255 1341 4.88 %
Rwork0.1877 26140 -
all0.191 --
obs-27481 80.679 %
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: 26.517 Å2
Baniso -1Baniso -2Baniso -3
1--0.094 Å2-0 Å20 Å2
2--0.046 Å2-0 Å2
3---0.048 Å2
Refinement stepCycle: LAST / Resolution: 2.28→77.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 77 408 5688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135425
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174847
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.6537374
X-RAY DIFFRACTIONr_angle_other_deg1.2691.57211166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5485660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67219.508325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57215805
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9941564
X-RAY DIFFRACTIONr_chiral_restr0.0670.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021278
X-RAY DIFFRACTIONr_nbd_refined0.1940.21115
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24853
X-RAY DIFFRACTIONr_nbtor_refined0.1590.22566
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2313
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.214
X-RAY DIFFRACTIONr_nbd_other0.1770.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1470.212
X-RAY DIFFRACTIONr_mcbond_it1.7742.6672656
X-RAY DIFFRACTIONr_mcbond_other1.7752.6652654
X-RAY DIFFRACTIONr_mcangle_it33.9823309
X-RAY DIFFRACTIONr_mcangle_other2.9993.9833310
X-RAY DIFFRACTIONr_scbond_it2.1042.9712769
X-RAY DIFFRACTIONr_scbond_other2.1042.9712770
X-RAY DIFFRACTIONr_scangle_it3.4734.3414065
X-RAY DIFFRACTIONr_scangle_other3.4724.3414066
X-RAY DIFFRACTIONr_lrange_it5.73231.0966156
X-RAY DIFFRACTIONr_lrange_other5.73231.1016157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.3390.304580.2031384X-RAY DIFFRACTION57.9582
2.339-2.4030.317770.2191441X-RAY DIFFRACTION62.3153
2.403-2.4730.303740.2181481X-RAY DIFFRACTION66.4814
2.473-2.5490.305930.2121492X-RAY DIFFRACTION69.3654
2.549-2.6320.257690.1981550X-RAY DIFFRACTION73.1586
2.632-2.7240.322630.2661084X-RAY DIFFRACTION53.0773
2.724-2.8270.376930.2231651X-RAY DIFFRACTION83.8462
2.827-2.9420.304770.2131743X-RAY DIFFRACTION90.0544
2.942-3.0730.31990.2111743X-RAY DIFFRACTION96.2886
3.073-3.2230.278680.2061775X-RAY DIFFRACTION100
3.223-3.3970.25850.1981676X-RAY DIFFRACTION100
3.397-3.6020.254620.1831221X-RAY DIFFRACTION77.7576
3.602-3.850.245630.1751231X-RAY DIFFRACTION81.8987
3.85-4.1580.208590.1671137X-RAY DIFFRACTION82.4259
4.158-4.5540.245640.1461306X-RAY DIFFRACTION100
4.554-5.0890.197730.1491160X-RAY DIFFRACTION100
5.089-5.8720.228570.1791048X-RAY DIFFRACTION99.9096
5.872-7.1820.228440.177884X-RAY DIFFRACTION99.7849
7.182-100.152430.135706X-RAY DIFFRACTION100
8-100.183200.183427X-RAY DIFFRACTION99.1131

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