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- PDB-5e0b: Crystal structure of the complex of Peptidoglycan recognition pro... -

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Basic information

Entry
Database: PDB / ID: 5e0b
TitleCrystal structure of the complex of Peptidoglycan recognition protein PGRP-S with N-Acetyl Muramic acid at 2.6 A resolution
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE SYSTEM / Peptidoglycan / N-Acetyl Muramic acid
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
N-acetyl-beta-muramic acid / L(+)-TARTARIC ACID / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSharma, P. / Yamini, S. / Dube, D. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of Peptidoglycan recognition protein PGRP-S with N-Acetyl Muramic acid at 2.6 A resolution
Authors: Sharma, P. / Yamini, S. / Dube, D. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: 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 / pdbx_prerelease_seq / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.symmetry_operation
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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)76,5817
Polymers76,0464
Non-polymers5353
Water6,107339
1
A: Peptidoglycan recognition protein 1
B: Peptidoglycan recognition protein 1


Theoretical massNumber of molelcules
Total (without water)38,0232
Polymers38,0232
Non-polymers00
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)38,5585
Polymers38,0232
Non-polymers5353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.205, 101.510, 162.998
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-315-

HOH

21D-346-

HOH

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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-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Sugar ChemComp-AMU / N-acetyl-beta-muramic acid / N-acetyl-muramic acid / BETA-N-ACETYLMURAMIC ACID


Type: D-saccharide, beta linking / Mass: 293.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO8
IdentifierTypeProgram
b-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 339 / 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

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M SODIUM POTASSIUM TARTRATE, 10% PEG 3350, PH 7.8
PH range: 7.8

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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: Jul 6, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 22829 / Num. obs: 22829 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 59.5 Å2 / Net I/σ(I): 11
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C2X

3c2x


Resolution: 2.6→19.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3051954.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1109 4.9 %RANDOM
Rwork0.226 ---
obs0.226 22829 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.7985 Å2 / ksol: 0.300484 e/Å3
Displacement parametersBiso mean: 49.9 Å2
Baniso -1Baniso -2Baniso -3
1-26.13 Å20 Å20 Å2
2---22.7 Å20 Å2
3----3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.41 Å
Refinement stepCycle: 1 / Resolution: 2.6→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 376 0 3050
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 175 4.7 %
Rwork0.316 3582 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION3CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION4CNS_TOPPAR/carbohydrate.paramCNS_TOPPAR/carbohydrate.top
X-RAY DIFFRACTION5lig.parlig.top

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