1Z5N

Crystal structure of MTA/AdoHcy nucleosidase Glu12Gln mutant complexed with 5-methylthioribose and adenine

• PDB DOI: https://doi.org/10.2210/pdb1Z5N/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-03-18 Released: 2005-10-04 
• Deposition Author(s): Lee, J.E., Smith, G.D., Horvatin, C., Huang, D.J.T., Cornell, K.A., Riscoe, M.K., Howell, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

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: 51.6 kDa 
• Atom Count: 3,605 
• Modelled Residue Count: 466 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MTA/SAH nucleosidase	A, B	242	Escherichia coli	Mutation(s): 1  Gene Names: mtnN, mtn, pfs EC: 3.2.2.9
UniProt
Find proteins for P0AF12 (Escherichia coli (strain K12)) Explore P0AF12  Go to UniProtKB:  P0AF12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR1	C [auth A], E [auth B]	5-S-methyl-5-thio-alpha-D-ribofuranose C6 H12 O4 S OLVVOVIFTBSBBH-KAZBKCHUSA-N
ADE	D [auth A], F [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADE	Binding MOAD:  1Z5N	Ki: 3.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.68	α = 90
b = 69.46	β = 90
c = 128.36	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
d*TREK	data reduction
CNS	refinement
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-04 
Deposition Author(s): Lee, J.E., Smith, G.D., Horvatin, C., Huang, D.J.T., Cornell, K.A., Riscoe, M.K., Howell, P.L.

Revision History  

• Version 1.0: 2005-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-08-23
  Changes: Data collection, Refinement description