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- PDB-4orv: Crystal structure of the ternary complex of camel peptidoglycan r... -

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Basic information

Entry
Database: PDB / ID: 4orv
TitleCrystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / IMMUNE RESPONSE / SECRETED / ANTIMICROBIAL / PGRP-S / ANTIBIOTIC / PEPTIDOGLYCAN BINDING / IMMUNE SYSTEM'
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
L(+)-TARTARIC ACID / 7-phenylheptanoic acid / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYamini, S. / Sharma, P. / Yadav, S.P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the ternary complex of camel peptidoglycan recognition protein PGRP-S with 7- phenylheptanoic acid and N- acetylglucosamine at 2.50 A resolution
Authors: Yamini, S. / Sharma, P. / Yadav, S.P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)76,9229
Polymers76,0464
Non-polymers8765
Water7,008389
1
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2293
Polymers38,0232
Non-polymers2061
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)38,6936
Polymers38,0232
Non-polymers6704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.535, 101.560, 163.457
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11C-352-

HOH

21C-370-

HOH

31D-324-

HOH

41D-369-

HOH

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Components

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Protein / Sugars , 2 types, 5 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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 393 molecules

#2: Chemical ChemComp-XXC / 7-phenylheptanoic acid


Mass: 206.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18O2
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% glycerol, 6% PEG3350, pH 7.8, 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: Dec 9, 2013 / 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: 2.5→50 Å / Num. all: 23666 / Num. obs: 23666 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 53.6 Å2 / Rsym value: 0.143 / Net I/σ(I): 15.5
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.59 / % possible all: 84.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2X

3c2x


Resolution: 2.5→39.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4388027.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1198 4.8 %RANDOM
Rwork0.21 ---
all0.211 23666 --
obs0.21 23666 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1014 Å2 / ksol: 0.315341 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1-35.18 Å20 Å20 Å2
2---22.86 Å20 Å2
3----12.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 61 389 5798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d1.34
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 160 4.8 %
Rwork0.297 3207 -
obs--78 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5lig.paramlig.top

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