6WUR | pdb_00006wur

Crystal structure of PRL-2 phosphatase C101D mutant in complex with the Bateman domain of CNNM3 magnesium transporter

• PDB DOI: https://doi.org/10.2210/pdb6WUR/pdb

• Classification: METAL TRANSPORT/HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-05-05 Released: 2020-07-01 
• Deposition Author(s): Kozlov, G., Gehring, K.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PRL phosphatase C104D mutant in complex with the Bateman domain of CNNM magnesium transporter

Kozlov, G., Funato, Y., Chen, S., Zhang, Z., Illes, K., Miki, H., Gehring, K.

(2020) J Biological Chem 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.53 kDa 
• Atom Count: 2,242 
• Modeled Residue Count: 307 
• Deposited Residue Count: 344 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein tyrosine phosphatase type IVA 2	A	189	Homo sapiens	Mutation(s): 1  Gene Names: PTP4A2, PRL2, PTPCAAX2, BM-008 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q12974 (Homo sapiens) Explore Q12974  Go to UniProtKB:  Q12974
PHAROS:  Q12974 GTEx:  ENSG00000184007

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Metal transporter CNNM3	B	155	Homo sapiens	Mutation(s): 0  Gene Names: CNNM3, ACDP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NE01 (Homo sapiens) Explore Q8NE01  Go to UniProtKB:  Q8NE01
PHAROS:  Q8NE01 GTEx:  ENSG00000168763

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.295 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.857	α = 90
b = 124.544	β = 90
c = 153.413	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Kozlov, G., Gehring, K.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RPGIN2014-04686

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description