9DRF

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (DTP bound, P21 form)

• PDB DOI: https://doi.org/10.2210/pdb9DRF/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-25 Released: 2024-10-02 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.217 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (DTP bound, P21 form)

Liu, L., Lovell, S., Buchko, G.W., Battaile, K.P.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 202.04 kDa 
• Atom Count: 13,581 
• Modelled Residue Count: 1,582 
• Deposited Residue Count: 1,744 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose pyrophosphatase	A, B, C, D, E, F, G, H	218	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: KPHS_45750 EC: 3.6.1.13
UniProt
Find proteins for A0A0H3GVQ7 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GVQ7  Go to UniProtKB:  A0A0H3GVQ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP (Subject of Investigation/LOI)	I [auth A], J [auth B], L [auth C], M [auth C], O [auth E], P [auth E], T [auth G], U [auth G]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
MG (Subject of Investigation/LOI)	K [auth B], N [auth C], Q [auth E], R [auth F], S [auth F], V [auth G], W [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.217 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.034	α = 90
b = 80.131	β = 90.13
c = 116.189	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release