3QJ1

Crystal structure of camel peptidoglycan recognition protein, PGRP-S with a trapped diethylene glycol in the ligand diffusion channel at 3.2 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3QJ1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Camelus dromedarius
• Mutation(s): No 


• Deposited: 2011-01-28 Released: 2011-02-16 
• Deposition Author(s): Sharma, P., Yamini, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

Crystal structure of camel peptidoglycan recognition protein, PGRP-S with a trapped diethylene glycol in the ligand diffusion channel at 3.2 A resolution

Sharma, P., Yamini, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.39 kDa 
• Atom Count: 5,452 
• Modelled Residue Count: 684 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein 1	A, B, C, D	171	Camelus dromedarius	Mutation(s): 0  EC: 3.5.1.28
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12  Go to UniProtKB:  Q9GK12

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	F [auth C]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	G [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.54	α = 90
b = 100.596	β = 90
c = 163.139	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-16 
Deposition Author(s): Sharma, P., Yamini, S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary