1WTA

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)

• PDB DOI: https://doi.org/10.2210/pdb1WTA/pdb

• Classification: TRANSFERASE
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-11-18 Released: 2006-02-07 
• Deposition Author(s): Tsunoda, M., Murakami, Y., Nakamura, K.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.196 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine from Aeropyrum pernix (R32 form)

Tsunoda, M., Murakami, Y., Nakamura, K.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 31.01 kDa 
• Atom Count: 2,507 
• Modelled Residue Count: 273 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine phosphorylase	A	275	Aeropyrum pernix K1	Mutation(s): 0  EC: 2.4.2.28
UniProt
Find proteins for Q9YAQ8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YAQ8  Go to UniProtKB:  Q9YAQ8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	C [auth A]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.196 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.15	α = 90
b = 78.15	β = 90
c = 230.43	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-07 
Deposition Author(s): Tsunoda, M., Murakami, Y., Nakamura, K.T.

Revision History  

• Version 1.0: 2006-02-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.4: 2017-11-01
  Changes: Derived calculations
• Version 1.5: 2024-11-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary