3K13

Structure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron

• PDB DOI: https://doi.org/10.2210/pdb3K13/pdb

• Classification: TRANSFERASE
• Organism(s): Bacteroides thetaiotaomicron
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-09-25 Released: 2009-12-22 
• Deposition Author(s): Cuff, M.E., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.188 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Structure of the pterin-binding domain MeTr of 5-methyltetrahydrofolate-homocysteine methyltransferase from Bacteroides thetaiotaomicron

Cuff, M.E., Li, H., Cobb, G., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 103.46 kDa 
• Atom Count: 7,727 
• Modelled Residue Count: 859 
• Deposited Residue Count: 900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-methyltetrahydrofolate-homocysteine methyltransferase	A, B, C	300	Bacteroides thetaiotaomicron	Mutation(s): 0  Gene Names: BT_0180
UniProt
Find proteins for Q8ABD0 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8ABD0  Go to UniProtKB:  Q8ABD0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THH	E [auth A], M [auth B], T [auth C]	N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID C20 H25 N7 O6 ZNOVTXRBGFNYRX-STQMWFEESA-N
GOL	D [auth A], F [auth A], I [auth A], K [auth B], L [auth B], O [auth B], P [auth B], R [auth C], S [auth C], V [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	G [auth A], H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	J [auth A], N [auth B], Q [auth B], U [auth C], W [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.188 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.652	α = 90
b = 79.992	β = 90.12
c = 127.068	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-22 
Deposition Author(s): Cuff, M.E., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description