9E9L | pdb_00009e9l

Vanadate-bound Putative Ancestral Protein Tyrosine Phosphatase ShufPTP - Intermediate p-loop Conformation

• PDB DOI: https://doi.org/10.2210/pdb9E9L/pdb

• Classification: HYDROLASE
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-08 Released: 2024-12-11 
• Deposition Author(s): Denson, J.M., Shen, R., Hengge, A.C., Johnson, S.J.
• Funding Organization(s): Other government

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

Yehorova, D., Alansson, N., Shen, R., Denson, J.M., Robinson, M., Risso, V.A., Ramirez Molina, N., Loria, J.P., Gaucher, E.A., Sanchez-Ruiz, J.M., Hengge, A.C., Johnson, S.J., Kamerlin, S.C.L.

(2025) JACS Au 

• DOI: https://doi.org/10.1021/jacsau.5c00756

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 17.83 kDa 
• Atom Count: 1,229 
• Modeled Residue Count: 149 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ShufPTP	A	150	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VO4 (Subject of Investigation/LOI)	D [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.718	α = 90
b = 85.718	β = 90
c = 32.374	γ = 120

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Denson, J.M., Shen, R., Hengge, A.C., Johnson, S.J.

---

Funding Organization	Location	Grant Number
Other government	United States	--

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-12-24
  Changes: Database references