5RKZ

PanDDA analysis group deposition of ground-state model of human NUDT22 screened against the DSPL fragment library by X-ray Crystallography

• PDB DOI: https://doi.org/10.2210/pdb5RKZ/pdb
• Deposition Group: G_1002129 (ground state) ExploreG_1002129

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-19 Released: 2020-07-22 
• Deposition Author(s): Diaz-Saez, L., Talon, R., Krojer, T., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.V.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

PanDDA analysis group deposition of ground-state model

Diaz-Saez, L., Talon, R., Krojer, T., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.V.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 33.02 kDa 
• Atom Count: 2,419 
• Modelled Residue Count: 291 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine diphosphate glucose pyrophosphatase NUDT22	A	304	Homo sapiens	Mutation(s): 0  Gene Names: NUDT22, PP11246 EC: 3.6.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BRQ3 (Homo sapiens) Explore Q9BRQ3  Go to UniProtKB:  Q9BRQ3
PHAROS:  Q9BRQ3 GTEx:  ENSG00000149761

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	B [auth A], C [auth A], D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.55	α = 90
b = 52.39	β = 90
c = 101.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Diaz-Saez, L., Talon, R., Krojer, T., Burgess-Brown, N.A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F., Huber, K.V.M.

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references