3PU9

Crystal structure of serine/threonine phosphatase Sphaerobacter thermophilus DSM 20745

• PDB DOI: https://doi.org/10.2210/pdb3PU9/pdb

• Classification: TRANSFERASE
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-03 Released: 2010-12-22 
• Deposition Author(s): Nocek, B., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.217 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Crystal structure of serine/threonine phosphatase Sphaerobacter thermophilus DSM 20745

Nocek, B., Tesar, C., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 51.41 kDa 
• Atom Count: 3,867 
• Modelled Residue Count: 472 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein serine/threonine phosphatase	A, B	242	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_0969
UniProt
Find proteins for D1C2D8 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C2D8  Go to UniProtKB:  D1C2D8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.217 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.168	α = 90
b = 54.713	β = 99.51
c = 63.262	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELX	model building
ARP/wARP	model building
CCP4	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Nocek, B., Tesar, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-08-08
  Changes: Other
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary