2OTD | pdb_00002otd

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

• PDB DOI: https://doi.org/10.2210/pdb2OTD/pdb

• Classification: HYDROLASE
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2007-02-07 Released: 2007-03-06 
• Deposition Author(s): Zhang, R., Wu, R., Clancy, S., Jiang, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

Zhang, R., Wu, R., Clancy, S., Jiang, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 111.09 kDa 
• Atom Count: 7,764 
• Modeled Residue Count: 980 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerophosphodiester phosphodiesterase	A, B, C, D	247	Shigella flexneri	Mutation(s): 7  Gene Names: ugpQ, SF3466, S_4296 EC: 3.1.4.1
UniProt
Find proteins for A0A0H2V2B5 (Shigella flexneri) Explore A0A0H2V2B5  Go to UniProtKB:  A0A0H2V2B5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth B], G [auth C], H [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.617	α = 90
b = 82.185	β = 90
c = 223.202	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Zhang, R., Wu, R., Clancy, S., Jiang, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary