9DT7 | pdb_00009dt7

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (5-O-phosphono-alpha-D-ribofuranose bound)

• PDB DOI: https://doi.org/10.2210/pdb9DT7/pdb

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


• Deposited: 2024-09-30 Released: 2024-10-09 
• 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: 1.15 Å
• R-Value Free: 
  0.152 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (5-O-phosphono-alpha-D-ribofuranose bound)

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

Macromolecule Content 

• Total Structure Weight: 49.99 kDa 
• Atom Count: 3,944 
• Modeled Residue Count: 408 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose pyrophosphatase	A, B	218	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: KPHS_45750 EC: 3.6.1.13
UniProt
Find proteins for B5XU49 (Klebsiella pneumoniae (strain 342)) Explore B5XU49  Go to UniProtKB:  B5XU49

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HSX (Subject of Investigation/LOI)	E [auth B], F [auth B]	5-O-phosphono-alpha-D-ribofuranose C5 H11 O8 P KTVPXOYAKDPRHY-AIHAYLRMSA-N
MG (Subject of Investigation/LOI)	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.152 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39DT7

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.509	α = 90
b = 79.74	β = 90
c = 91.709	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: 2024-10-09 
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: 2024-10-09
  Type: Initial release