9DSZ

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

PDB DOI: https://doi.org/10.2210/pdb9DSZ/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.233
R-Value Work: 0.196
R-Value Observed: 0.198

Starting Model: experimental
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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 (DTP bound)

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

To be published.

Macromolecule Content

Total Structure Weight: 202.12 kDa
Atom Count: 13,459
Modelled Residue Count: 1,568
Deposited Residue Count: 1,744
Unique protein chains: 1

Macromolecules

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(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 A0A0H3GVQ7 (Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)) Explore A0A0H3GVQ7 Go to UniProtKB: A0A0H3GVQ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3GVQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTP (Subject of Investigation/LOI) Query on DTP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain X [auth H] SDF format, chain Y [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], X [auth H], Y [auth H]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain X [auth H] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain X [auth H] Focus chain Y [auth H]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain Z [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain Z [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], U [auth F], V [auth G], W [auth G], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain Z [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.233
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M39DSZ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.843	α = 90
b = 79.311	β = 90.3
c = 115.827	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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)

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