4G41 | pdb_00004g41

Crystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin

• PDB DOI: https://doi.org/10.2210/pdb4G41/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes ATCC 10782
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-15 Released: 2012-09-12 
• Deposition Author(s): Ponniah, K., Norris, G.E., Anderson, B.F., Brown, R.L., Tyler, P.C., Evans, G.B., Frohlich, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of s-adenosylhomocysteine nucleosidase from streptococcus pyogenes in complex with 5-methylthiotubericidin;

Ponniah, K., Norris, G.E., Anderson, B.F., Brown, R.L., Tyler, P.C., Evans, G.B., Frohlich, R.

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: 50.7 kDa 
• Atom Count: 4,421 
• Modeled Residue Count: 472 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MTA/SAH nucleosidase	A, B	236	Streptococcus pyogenes ATCC 10782	Mutation(s): 0  Gene Names: HMPREF0841_1463, mtn N, mtnN EC: 3.2.2.16 (PDB Primary Data), 3.2.2.9 (PDB Primary Data)
UniProt
Find proteins for A0A0H2UTC3 (Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)) Explore A0A0H2UTC3  Go to UniProtKB:  A0A0H2UTC3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA	C [auth B]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.735	α = 90
b = 72.345	β = 90
c = 116.246	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Ponniah, K., Norris, G.E., Anderson, B.F., Brown, R.L., Tyler, P.C., Evans, G.B., Frohlich, R.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-04-03
  Changes: Refinement description