3LDG | pdb_00003ldg

Crystal structure of SMU.472, a putative methyltransferase complexed with SAH

• PDB DOI: https://doi.org/10.2210/pdb3LDG/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus mutans UA159
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-13 Released: 2011-01-19 
• Deposition Author(s): Wang, K.-T., Su, X.-D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Crystal structure of SMU.472 complexed with SAH

Wang, K.-T., Su, X.-D.

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)

Macromolecule Content 

• Total Structure Weight: 44.4 kDa 
• Atom Count: 3,392 
• Modeled Residue Count: 377 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein SMU.472	A	384	Streptococcus mutans UA159	Mutation(s): 0  Gene Names: SMU_472
UniProt
Find proteins for Q8DVL0 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DVL0  Go to UniProtKB:  Q8DVL0

Small Molecules

Ligands 1 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

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: 1.96 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.251	α = 90
b = 67.348	β = 90
c = 91.848	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Wang, K.-T., Su, X.-D.

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary