5D2U | pdb_00005d2u

Crystal structure of tPphA Variant - H39A

• PDB DOI: https://doi.org/10.2210/pdb5D2U/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Thermosynechococcus vestitus BP-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-08-06 Released: 2016-05-04 
• Deposition Author(s): Su, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Structural and Biochemical Characterization of a Cyanobacterial PP2C Phosphatase Reveals Insights into Catalytic Mechanism and Substrate Recognition

Si, Y., Yuan, Y., Wang, Y., Gao, J., Hu, Y., Feng, S., Su, J.

(2016) Catalysts 

• DOI: https://doi.org/10.3390/catal6050060

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: 27.11 kDa 
• Atom Count: 1,865 
• Modeled Residue Count: 240 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein serin-threonin phosphatase	A	243	Thermosynechococcus vestitus BP-1	Mutation(s): 1  Gene Names: tlr2243
UniProt
Find proteins for Q8DGS1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DGS1  Go to UniProtKB:  Q8DGS1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.042	α = 90
b = 153.872	β = 90
c = 82.761	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Su, J.

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description