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- PDB-3uil: Crystal Structure of the complex of PGRP-S with lauric acid at 2.... -

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Basic information

Entry
Database: PDB / ID: 3uil
TitleCrystal Structure of the complex of PGRP-S with lauric acid at 2.2 A resolution
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / Immune response / secreted / antimicrobial / PGRP / Antibiotic / Peptidoglycan Binding
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. / 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
LAURIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDube, D. / Sharma, P. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Arch.Biochem.Biophys. / Year: 2013
Title: Structural basis of the binding of fatty acids to peptidoglycan recognition protein, PGRP-S through second binding site
Authors: Sharma, P. / Yamini, S. / Dube, D. / Singh, A. / Mal, G. / Pandey, N. / Sinha, M. / Singh, A.K. / Dey, S. / Kaur, P. / Mitra, D.K. / Sharma, S. / Singh, T.P.
History
DepositionNov 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)76,3386
Polymers76,0464
Non-polymers2922
Water11,151619
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.000, 101.610, 163.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
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: 49.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10% PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2011 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→86.3 Å / Num. obs: 33252 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.2 Å2 / Rsym value: 0.086 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.26 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.455 / % possible all: 92.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
AMoREphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2X

3c2x


Resolution: 2.2→86.29 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.137 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1774 5.1 %RANDOM
Rwork0.227 ---
obs0.2324 33252 92.22 %-
all-33252 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 106.01 Å2 / Biso mean: 41.4233 Å2 / Biso min: 4.96 Å2
Baniso -1Baniso -2Baniso -3
1-4.02 Å20 Å20 Å2
2---3.26 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→86.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5347 0 20 619 5986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0215525
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.9367532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7035680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67522.09268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03715816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4271564
X-RAY DIFFRACTIONr_chiral_restr0.1310.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214384
X-RAY DIFFRACTIONr_mcbond_it1.2221.53403
X-RAY DIFFRACTIONr_mcangle_it2.15625462
X-RAY DIFFRACTIONr_scbond_it3.12832122
X-RAY DIFFRACTIONr_scangle_it4.8284.52070
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.616 135 -
Rwork0.604 2433 -
all-2568 -
obs--92.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84450.1823-0.16030.72820.09791.5222-0.157-0.00780.0125-0.0388-0.00590.01260.00220.01150.16290.09620.0058-0.06650.0720.03560.0957-21.9592-36.8368-45.7377
21.56150.5669-0.33422.786-0.20150.57660.1012-0.00620.04370.05050.09850.22070.02260.024-0.19970.1672-0.068-0.09190.04240.03730.1217-35.6756-15.3157-60.4429
30.60230.04020.1570.9474-0.21131.04660.08260.0481-0.10620.0525-0.0250.1218-0.10590.0787-0.05770.16540.0303-0.02340.0289-0.01180.0801-26.2682-38.3619-8.3972
41.3328-0.05350.25061.7745-0.02130.9702-0.14510.1276-0.13530.21250.1365-0.091-0.09760.00530.00850.2030.0573-0.01760.0419-0.02760.0224-36.1942-12.7811-18.4917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 171
2X-RAY DIFFRACTION2B1 - 171
3X-RAY DIFFRACTION3C1 - 171
4X-RAY DIFFRACTION4D1 - 171
5X-RAY DIFFRACTION4D201 - 202

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