2PY6

Crystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2PY6/pdb

• Classification: TRANSFERASE
• Organism(s): Methylobacillus flagellatus KT
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-05-15 Released: 2007-05-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.224 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 

Literature

Crystal structure of Methyltransferase FkbM (YP_546752.1) from Methylobacillus flagellatus KT at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 46.9 kDa 
• Atom Count: 3,385 
• Modelled Residue Count: 375 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase FkbM	A	409	Methylobacillus flagellatus KT	Mutation(s): 7  Gene Names: YP_546752.1, Mfla_2648 EC: 2.1.1
UniProt
Find proteins for Q1GXX6 (Methylobacillus flagellatus (strain ATCC 51484 / DSM 6875 / VKM B-1610 / KT)) Explore Q1GXX6  Go to UniProtKB:  Q1GXX6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	G [auth A]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.15 Å
• R-Value Free: 0.224 
• R-Value Work: 0.166 
• R-Value Observed: 0.169 
• Space Group: I 2 2 2
• Diffraction Data: https://doi.org/10.18430/M32PY6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.66	α = 90
b = 119.17	β = 90
c = 122.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.7: 2024-10-30
  Changes: Data collection, Structure summary