8WS2 | pdb_00008ws2

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine

• PDB DOI: https://doi.org/10.2210/pdb8WS2/pdb

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


• Deposited: 2023-10-16 Released: 2024-10-09 
• Deposition Author(s): Iizuka, Y., Kikuchi, M., Yamauchi, T., Tsunoda, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free: 
  0.166 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.142 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine

Iizuka, Y., Kikuchi, M., Yamauchi, T., Tsunoda, M.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.53 kDa 
• Atom Count: 2,474 
• Modeled Residue Count: 273 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-methyl-5'-thioadenosine phosphorylase	A	275	Aeropyrum pernix K1	Mutation(s): 0  Gene Names: mtnP, APE_1885 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTA (Subject of Investigation/LOI)	C [auth A]	5'-DEOXY-5'-METHYLTHIOADENOSINE C11 H15 N5 O3 S WUUGFSXJNOTRMR-IOSLPCCCSA-N
PGE	D [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	E [auth A], F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.22 Å
• R-Value Free:  0.166 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.142 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.646	α = 90
b = 77.646	β = 90
c = 230.39	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
MOLREP	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Iizuka, Y., Kikuchi, M., Yamauchi, T., Tsunoda, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release