2WR8 | pdb_00002wr8

Structure of Pyrococcus horikoshii SAM hydroxide adenosyltransferase in complex with SAH

• PDB DOI: https://doi.org/10.2210/pdb2WR8/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-31 Released: 2009-09-22 
• Deposition Author(s): McMahon, S.A., Deng, H., O'Hagan, D., Johnson, K.A., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.217 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Mechanistic Insights Into Water Activation in Sam Hydroxide Adenosyltransferase (Duf-62).

Deng, H., Mcmahon, S.A., Eustaquio, A.S., Moore, B.S., Naismith, J.H., O'Hagan, D.

(2009) Chembiochem 10: 2455

• PubMed: 19739191 
• DOI: https://doi.org/10.1002/cbic.200900369
• Primary Citation Related Structures: 
  2WR8

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Organizational Affiliation: 
• Centre for Biomolecular Sciences, School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, UK.

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)

Macromolecule Content 

• Total Structure Weight: 29.32 kDa 
• Atom Count: 2,179 
• Modeled Residue Count: 258 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE UNCHARACTERIZED PROTEIN PH0463	A	259	Pyrococcus horikoshii OT3	Mutation(s): 0  EC: 3.13.2.3
UniProt
Find proteins for O58212 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58212  Go to UniProtKB:  O58212

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.217 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.561	α = 90
b = 65.561	β = 90
c = 142.685	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): McMahon, S.A., Deng, H., O'Hagan, D., Johnson, K.A., Naismith, J.H.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2025-12-10
  Changes: Data collection, Structure summary