2DFJ | pdb_00002dfj

Crystal Structure of the Diadenosine Tetraphosphate Hydrolase from Shigella flexneri 2a

• PDB DOI: https://doi.org/10.2210/pdb2DFJ/pdb

• Classification: HYDROLASE
• Organism(s): Shigella flexneri 2a
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-03-02 Released: 2006-12-05 
• Deposition Author(s): Wang, Q.H., Hu, W.X., Bi, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.268 (Depositor) 
• R-Value Work: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Crystal structure of the diadenosine tetraphosphate hydrolase from Shigella flexneri 2a

Wang, Q.H., Hu, W.X., Gao, W., Bi, R.C.

(2006) Proteins 65: 1032-1035

• PubMed: 17006950 
• DOI: https://doi.org/10.1002/prot.21106
• Primary Citation Related Structures: 
  2DFJ

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Organizational Affiliation: 
• Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 62.86 kDa 
• Atom Count: 4,313 
• Modeled Residue Count: 534 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
diadenosinetetraphosphatase	A, B	280	Shigella flexneri 2a	Mutation(s): 0  EC: 3.6.1.41
UniProt
Find proteins for Q83SQ2 (Shigella flexneri) Explore Q83SQ2  Go to UniProtKB:  Q83SQ2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth B], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.268 (Depositor) 
• R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.498	α = 90
b = 54.965	β = 129.14
c = 119.203	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Wang, Q.H., Hu, W.X., Bi, R.C.

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations