3OCC

Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

• PDB DOI: https://doi.org/10.2210/pdb3OCC/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pseudotuberculosis YPIII
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-09 Released: 2010-11-10 
• Deposition Author(s): Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.181 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Starting Model: experimental

Literature

crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 157.96 kDa 
• Atom Count: 12,217 
• Modelled Residue Count: 1,424 
• Deposited Residue Count: 1,434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase deoD-type	A, B, C, D, E, F	239	Yersinia pseudotuberculosis YPIII	Mutation(s): 0  Gene Names: deoD, YPK_3624 EC: 2.4.2.1
UniProt
Find proteins for B1JL34 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII)) Explore B1JL34  Go to UniProtKB:  B1JL34

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIH	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one C12 H17 N4 O3 AFNHHLILYQEHKK-BDAKNGLRSA-O
PO4	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.181 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.647	α = 90
b = 109.829	β = 90
c = 154.747	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-12-12
  Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description