3LKD

Crystal Structure of the type I restriction-modification system methyltransferase subunit from Streptococcus thermophilus, Northeast Structural Genomics Consortium Target SuR80

• PDB DOI: https://doi.org/10.2210/pdb3LKD/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus thermophilus LMG 18311
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-27 Released: 2010-02-09 
• Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Mao, M., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 

Literature

Northeast Structural Genomics Consortium Target SuR80

Vorobiev, S., Su, M., Seetharaman, J., Mao, M., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 124.39 kDa 
• Atom Count: 7,930 
• Modelled Residue Count: 940 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type I restriction-modification system methyltransferase subunit	A, B	542	Streptococcus thermophilus LMG 18311	Mutation(s): 0  Gene Names: hsdM1, stu0711
UniProt
Find proteins for Q5M500 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)) Explore Q5M500  Go to UniProtKB:  Q5M500

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.210 
• R-Value Work: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.866	α = 90
b = 83.128	β = 98.13
c = 96.678	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AutoSol	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Vorobiev, S., Su, M., Seetharaman, J., Mao, M., Xiao, R., Foote, E.L., Ciccosanti, C., Wang, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description