4O29 | pdb_00004o29

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE from Pyrobaculum aerophilum in COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE

• PDB DOI: https://doi.org/10.2210/pdb4O29/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrobaculum aerophilum str. IM2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-17 Released: 2014-01-15 
• Deposition Author(s): Sawaya, M.R., Yeates, T.O., Griffith, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.261 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structure of L-isoaspartyl (D-aspartyl) Methyltransferase

Griffith, S.C.

(2002) Thesis University of California, Los Angeles: 93-107

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.62 kDa 
• Atom Count: 1,635 
• Modeled Residue Count: 207 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-L-isoaspartate O-methyltransferase	A	208	Pyrobaculum aerophilum str. IM2	Mutation(s): 0  Gene Names: PAE0701, pcm, PIMT EC: 2.1.1.77
UniProt
Find proteins for Q8ZYN0 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZYN0  Go to UniProtKB:  Q8ZYN0

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: 2.90 Å
• R-Value Free:  0.261 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.72	α = 90
b = 35.67	β = 100.31
c = 66.29	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
EPMR	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Sawaya, M.R., Yeates, T.O., Griffith, S.C.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description