4HTF | pdb_00004htf

Crystal structure of S-adenosylmethionine-dependent methyltransferase from Escherichia coli in complex with S-adenosylmethionine.

• PDB DOI: https://doi.org/10.2210/pdb4HTF/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-01 Released: 2012-11-21 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.201 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal structure of S-adenosylmethionine-dependent methyltransferase from Escherichia coli in complex with S-adenosylmethionine.

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 67.43 kDa 
• Atom Count: 4,454 
• Modeled Residue Count: 491 
• Deposited Residue Count: 570 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine-dependent methyltransferase	A	285	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: BAB34427, ECs1004, smtA, Z1268 EC: 2.1.1
UniProt
Find proteins for Q8XDG3 (Escherichia coli O157:H7) Explore Q8XDG3  Go to UniProtKB:  Q8XDG3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine-dependent methyltransferase	B	285	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: BAB34427, ECs1004, smtA, Z1268 EC: 2.1.1
UniProt
Find proteins for Q8XDG3 (Escherichia coli O157:H7) Explore Q8XDG3  Go to UniProtKB:  Q8XDG3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], F [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
SO4	D [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	H [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.201 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34HTF

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.537	α = 90
b = 63.466	β = 90
c = 136.881	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-21 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary