5EPE | pdb_00005epe

Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine

• PDB DOI: https://doi.org/10.2210/pdb5EPE/pdb

• Classification: TRANSFERASE
• Organism(s): Thiobacillus denitrificans ATCC 25259
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-11 Released: 2015-11-25 
• Deposition Author(s): LaRowe, C., Shabalin, I.G., Kutner, J., Handing, K.B., Stead, M., Hillerich, B.S., Ahmed, M., Seidel, R., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.167 (Depositor), 0.166 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

Crystal structure of SAM-dependent methyltransferase from Thiobacillus denitrificans in complex with S-Adenosyl-L-homocysteine

LaRowe, C., Shabalin, I.G., Kutner, J., Handing, K.B., Minor, W.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 27.85 kDa 
• Atom Count: 2,207 
• Modeled Residue Count: 248 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent methyltransferase	A	248	Thiobacillus denitrificans ATCC 25259	Mutation(s): 0  Gene Names: Tbd_1076 EC: 2.1.1
UniProt
Find proteins for Q3SJX0 (Thiobacillus denitrificans (strain ATCC 25259 / T1)) Explore Q3SJX0  Go to UniProtKB:  Q3SJX0

Small Molecules

Ligands 2 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
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.90 Å
• R-Value Free:  0.167 (Depositor), 0.166 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m3159c

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.536	α = 90
b = 157.536	β = 90
c = 157.536	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): LaRowe, C., Shabalin, I.G., Kutner, J., Handing, K.B., Stead, M., Hillerich, B.S., Ahmed, M., Seidel, R., Bonanno, J., 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/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2015-12-23
  Changes: Other
• Version 1.2: 2016-02-24
  Changes: Other
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.4: 2018-08-15
  Changes: Data collection, Database references
• Version 1.5: 2019-12-04
  Changes: Author supporting evidence
• Version 1.6: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2024-11-06
  Changes: Data collection, Structure summary