1Y8C | pdb_00001y8c

Crystal structure of a S-adenosylmethionine-dependent methyltransferase from Clostridium acetobutylicum ATCC 824

• PDB DOI: https://doi.org/10.2210/pdb1Y8C/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridium acetobutylicum ATCC 824
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-11 Released: 2004-12-28 
• Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.275 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a S-adenosylmethionine-dependent methyltransferase from Clostridium acetobutylicum ATCC 824

Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.43 kDa 
• Atom Count: 2,109 
• Modeled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine-dependent methyltransferase	A	246	Clostridium acetobutylicum ATCC 824	Mutation(s): 2  Gene Names: CAC2371, 1118554
UniProt
Find proteins for Q97GJ5 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)) Explore Q97GJ5  Go to UniProtKB:  Q97GJ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.275 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.918	α = 90
b = 67.918	β = 90
c = 134.499	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-28 
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary