3NNO | pdb_00003nno

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with Alpha-Rhamnose at 2.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NNO/pdb

• Classification: ANTIBIOTIC
• Organism(s): Camelus dromedarius
• Mutation(s): No 


• Deposited: 2010-06-24 Released: 2010-07-21 
• Deposition Author(s): Dube, D., Sharma, P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.193 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with Alpha-Rhamnose at 2.9 A resolution

Dube, D., Sharma, P., 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: 76.36 kDa 
• Atom Count: 5,513 
• Modeled 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
UniProt
Find proteins for Q9GK12 (Camelus dromedarius) Explore Q9GK12  Go to UniProtKB:  Q9GK12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAM	F [auth D]	alpha-L-rhamnopyranose C6 H12 O5 SHZGCJCMOBCMKK-HGVZOGFYSA-N
TLA	E [auth C]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.193 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.25	α = 90
b = 101.9	β = 90
c = 164.08	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
CNS	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Dube, D., Sharma, P., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-30
  Changes: Structure summary