5BP9 | pdb_00005bp9

Crystal structure of SAM-dependent methyltransferase from Bacteroides fragilis in complex with S-Adenosyl-L-homocysteine

• PDB DOI: https://doi.org/10.2210/pdb5BP9/pdb

• Classification: TRANSFERASE
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-27 Released: 2015-06-10 
• Deposition Author(s): Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Cymborowski, M.T., Mason, D.V., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

Crystal structure of SAM-dependent methyltransferase fromBacteroides fragilis in complex with S-Adenosyl-L-homocysteine

Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Cymborowski, M.T., Mason, D., Bonanno, J., Seidel, R., Almo, S.C., Minor, W.

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: 33.09 kDa 
• Atom Count: 2,320 
• Modeled Residue Count: 237 
• Deposited Residue Count: 281 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase protein	A	281	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF9343_1312
UniProt
Find proteins for Q5LFK0 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LFK0  Go to UniProtKB:  Q5LFK0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ETE	B [auth A]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C9 H20 O5 ZNYRFEPBTVGZDN-UHFFFAOYSA-N
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

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: 1.50 Å
• R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39013

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.732	α = 90
b = 70.66	β = 90
c = 78.743	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Cymborowski, M.T., Mason, D.V., Bonanno, J., Seidel, R., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

---

Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.3: 2024-10-09
  Changes: Data collection, Structure summary