3KU1 | pdb_00003ku1

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase, in complex with S-adenosyl-L-methionine

• PDB DOI: https://doi.org/10.2210/pdb3KU1/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-11-26 Released: 2009-12-22 
• Deposition Author(s): Ta, M.H., Kim, K.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.296 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA (m1A22) methyltransferase in complex with S-adenosyl-L-methionine

Ta, M.H., Kim, K.K.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PISA (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 201.32 kDa 
• Atom Count: 13,482 
• Modeled Residue Count: 1,712 
• Deposited Residue Count: 1,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent methyltransferase	A, B, C, D, E, F, G, H	225	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: SP_1610 EC: 2.1.1.36
UniProt
Find proteins for A0A0H2UR54 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UR54  Go to UniProtKB:  A0A0H2UR54

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	I [auth A], J [auth C], K [auth G], L [auth H]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.296 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.752	α = 90
b = 142.752	β = 90
c = 148.163	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Ta, M.H., Kim, K.K.

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description