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- PDB-2z9n: Crystal structure of cameline peptidoglycan recognition protein a... -

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Basic information

Entry
Database: PDB / ID: 2z9n
TitleCrystal structure of cameline peptidoglycan recognition protein at 3.2 A resolution
ComponentsPeptidoglycan recognition protein
KeywordsIMMUNE SYSTEM / crystal / complex / peptidoglycan recognition protein / Antibiotic / Antimicrobial / Immune response / Secreted
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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSharma, P. / Jain, R. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of cameline peptidoglycan recognition protein at 3.2 A resolution
Authors: Sharma, P. / Jain, R. / Singh, N. / Sharma, S. / Kaur, P. / Singh, T.P.
History
DepositionSep 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan recognition protein
B: Peptidoglycan recognition protein
C: Peptidoglycan recognition protein
D: Peptidoglycan recognition protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4967
Polymers76,0464
Non-polymers4503
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.855, 102.456, 164.043
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 / 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) / Secretion: Milk / References: UniProt: Q9GK12
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 2M Sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2007 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. obs: 12274 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.233 / Net I/σ(I): 6.9
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 11 / Num. unique all: 59370 / Rsym value: 0.43 / % possible all: 92.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.1refinement
DENZOdata reduction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2K

2r2k


Resolution: 3.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.258 1907 -
Rwork0.215 --
obs-12274 88.7 %
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 30 81 5459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
LS refinement shellResolution: 3.2→3.31 Å
RfactorNum. reflection% reflection
Rfree0.258 1907 -
Rwork0.215 --
obs-12274 92.2 %

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