9DRE | pdb_00009dre

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

PDB DOI: https://doi.org/10.2210/pdb9DRE/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.210 (Depositor), 0.216 (DCC)
R-Value Work:
0.175 (Depositor), 0.183 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 201.53 kDa
Atom Count: 13,700
Modeled Residue Count: 1,568
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose pyrophosphatase	A, B, C, D, E 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 B5XU49 (Klebsiella pneumoniae (strain 342)) Explore B5XU49 Go to UniProtKB: B5XU49
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5XU49
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain Q [auth F] SDF format, chain V [auth H] SDF format, chain T [auth G] SDF format, chain O [auth E] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth F] MOL2 format, chain V [auth H] MOL2 format, chain T [auth G] MOL2 format, chain O [auth E] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth F] mmCIF format, chain V [auth H] mmCIF format, chain T [auth G] mmCIF format, chain O [auth E] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] L [auth C] N [auth D] O [auth E] I [auth A], J [auth B], L [auth C], N [auth D], O [auth E], Q [auth F], T [auth G], V [auth H]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain T [auth G] Focus chain V [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain Q [auth F] Focus chain T [auth G] Focus chain V [auth H]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	K [auth B] M [auth C] P [auth E] R [auth F] S [auth F] K [auth B], M [auth C], P [auth E], R [auth F], S [auth F], U [auth G], W [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.210 (Depositor), 0.216 (DCC)
R-Value Work: 0.175 (Depositor), 0.183 (DCC)
R-Value Observed: 0.177 (Depositor)

Diffraction Data: https://doi.org/10.18430/m39dre

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.873	α = 90
b = 80.109	β = 90.12
c = 115.834	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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)

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