6IDM | pdb_00006idm

Crystal structure of Peptidoglycan recognition protein (PGRP-S) with Tartaric acid at 3.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6IDM/pdb

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


• Deposited: 2018-09-10 Released: 2018-09-26 
• Deposition Author(s): Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Peptidoglycan recognition protein (PGRP-S) with Tartaric acid at 3.20 A resolution

Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., 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: 74.16 kDa 
• Atom Count: 5,334 
• Modelled Residue Count: 664 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan recognition protein 1	A, B, C, D	166	Camelus dromedarius	Mutation(s): 0
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12  Go to UniProtKB:  Q9GK12

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	E [auth C]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.309	α = 90
b = 101.149	β = 90
c = 163.566	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Bairagya, H.R., Shokeen, A., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary