5BP7 | pdb_00005bp7

Crystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in complex with S-Adenosyl-L-homocysteine

• PDB DOI: https://doi.org/10.2210/pdb5BP7/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacter sulfurreducens PCA
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.223 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in complex with S-Adenosyl-L-homocysteine

Kutner, J., Shabalin, I.G., Mason, D., Handing, K.B., Gasiorowska, O.A., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.74 kDa 
• Atom Count: 6,172 
• Modeled Residue Count: 746 
• Deposited Residue Count: 813 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent methyltransferase	A, B, C	271	Geobacter sulfurreducens PCA	Mutation(s): 0  Gene Names: GSU2441
UniProt
Find proteins for Q74AD5 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74AD5  Go to UniProtKB:  Q74AD5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A], F [auth B], G [auth C]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
CL	E [auth A], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.223 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3C01Q

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.346	α = 90
b = 110.189	β = 90
c = 76.681	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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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: 2017-11-22
  Changes: 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, Refinement description, Structure summary