7XLF

Crystal structure of CH3-THF complex of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6

• PDB DOI: https://doi.org/10.2210/pdb7XLF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sphingobium sp. SYK-6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-04-21 Released: 2023-04-26 
• Deposition Author(s): Yu, H.Y., Senda, M., Senda, T.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Crystal structural of methylenetetrahydrofolate reductase from Sphingobium sp. SYK-6

Yu, H.Y., Senda, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.53 kDa 
• Atom Count: 4,777 
• Modelled Residue Count: 565 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methylenetetrahydrofolate reductase	A, B	288	Sphingobium sp. SYK-6	Mutation(s): 0  Gene Names: metF, SLG_12750 EC: 1.5.1.20 (PDB Primary Data), 1.5.1.54 (UniProt)
UniProt
Find proteins for G2IQS8 (Sphingobium sp. (strain NBRC 103272 / SYK-6)) Explore G2IQS8  Go to UniProtKB:  G2IQS8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
C2F (Subject of Investigation/LOI)	D [auth A], G [auth B]	5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID C20 H25 N7 O6 ZNOVTXRBGFNYRX-STQMWFEESA-N
PEG	E [auth A], H [auth B], I [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.217 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.127	α = 90
b = 170.347	β = 104.548
c = 45.151	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Yu, H.Y., Senda, M., Senda, T.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101001

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description