3OF3

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

• PDB DOI: https://doi.org/10.2210/pdb3OF3/pdb

• Classification: TRANSFERASE
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-13 Released: 2010-09-01 
• 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: 1.83 Å
• R-Value Free: 0.188 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Starting Model: experimental

Literature

Crystal structure of PNP with an inhibitor DADME_immH from Vibrio cholerae

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 318.16 kDa 
• Atom Count: 24,255 
• Modelled Residue Count: 2,878 
• Deposited Residue Count: 2,892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase deoD-type 1	A, B, C, D, E, F, G, H, I, J, K, L	241	Vibrio cholerae	Mutation(s): 0  Gene Names: deoD, deoD1, VC_2347 EC: 2.4.2.1
UniProt
Find proteins for Q9KPM0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KPM0  Go to UniProtKB:  Q9KPM0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIH	AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	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	BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.188 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.375	α = 90
b = 160.974	β = 90
c = 188.685	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: 2010-09-01 
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: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-12-12
  Changes: 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