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- PDB-6idm: Crystal structure of Peptidoglycan recognition protein (PGRP-S) w... -

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Basic information

Entry
Database: PDB / ID: 6idm
TitleCrystal structure of Peptidoglycan recognition protein (PGRP-S) with Tartaric acid at 3.20 A resolution
ComponentsPeptidoglycan recognition protein 1
KeywordsIMMUNE 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 / Peptidoglycan recognition protein 1
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBairagya, H.R. / Shokeen, A. / Sharma, P. / Singh, P.K. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of Peptidoglycan recognition protein (PGRP-S) with Tartaric acid at 3.20 A resolution
Authors: Bairagya, H.R. / Shokeen, A. / Sharma, P. / Singh, P.K. / Sharma, S. / Singh, T.P.
History
DepositionSep 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)74,1585
Polymers74,0084
Non-polymers1501
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Tetramer from crystallographic data
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.309, 101.149, 163.566
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: 18501.947 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 12% PEG 3350, 100mM Sodium potassium tartarate

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→47.99 Å / Num. obs: 12435 / % possible obs: 100 % / Redundancy: 6.88 % / Rsym value: 0.27 / Net I/σ(I): 4.27
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.63 / Num. unique obs: 853 / Rrim(I) all: 0.35 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RT4

3rt4


Resolution: 3.2→47.99 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.89 / SU B: 38.738 / SU ML: 0.596 / Cross valid method: THROUGHOUT / ESU R Free: 0.574 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2654 458 3.7 %RANDOM
Rwork0.19193 ---
obs0.19478 11977 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 75.203 Å2
Baniso -1Baniso -2Baniso -3
1-15.73 Å20 Å2-0 Å2
2---10.48 Å20 Å2
3----5.25 Å2
Refinement stepCycle: 1 / Resolution: 3.2→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5200 0 10 124 5334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195361
X-RAY DIFFRACTIONr_bond_other_d0.0020.024786
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9237296
X-RAY DIFFRACTIONr_angle_other_deg2.077311026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0545660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4621.846260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25115804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7651564
X-RAY DIFFRACTIONr_chiral_restr0.080.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216060
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.1887.6292652
X-RAY DIFFRACTIONr_mcbond_other10.197.6292651
X-RAY DIFFRACTIONr_mcangle_it16.33711.4343308
X-RAY DIFFRACTIONr_mcangle_other16.33511.4343309
X-RAY DIFFRACTIONr_scbond_it9.8647.8082709
X-RAY DIFFRACTIONr_scbond_other9.8697.8082706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.37711.6443987
X-RAY DIFFRACTIONr_long_range_B_refined14.49288.1486041
X-RAY DIFFRACTIONr_long_range_B_other14.47488.1536030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 33 -
Rwork0.34 853 -
obs--100 %

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