2YXE | pdb_00002yxe

Crystal structure of L-isoaspartyl protein carboxyl methyltranferase

• PDB DOI: https://doi.org/10.2210/pdb2YXE/pdb

• Classification: TRANSFERASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-26 Released: 2007-10-30 
• Deposition Author(s): Padmanabhan, B., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.231 (Depositor) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of L-isoaspartyl protein carboxyl methyltranferase

Padmanabhan, B., Bessho, Y., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.7 kDa 
• Atom Count: 3,518 
• Modeled Residue Count: 427 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-L-isoaspartate O-methyltransferase	A, B	215	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: pcm EC: 2.1.1.77
UniProt
Find proteins for Q57636 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57636  Go to UniProtKB:  Q57636

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.231 (Depositor) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.267	α = 90
b = 84.448	β = 90
c = 123.091	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Padmanabhan, B., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description