4FMW

Crystal structure of methyltransferase domain of human RNA (guanine-9-) methyltransferase domain containing protein 2

• PDB DOI: https://doi.org/10.2210/pdb4FMW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-18 Released: 2012-08-22 
• Deposition Author(s): Dong, A., Zeng, H., Loppnau, P., Tempel, W., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Crystal structure of methyltransferase domain of human RNA (guanine-9-) methyltransferase domain containing protein 2

Zeng, H., Dong, A., Loppnau, P., Tempel, W., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Wu, H.

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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.49 kDa 
• Atom Count: 3,054 
• Modelled Residue Count: 350 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA (guanine-9-)-methyltransferase domain-containing protein 2	A, B	197	Homo sapiens	Mutation(s): 0  Gene Names: RG9MTD2 EC: 2.1.1 (PDB Primary Data), 2.1.1.221 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBZ6 (Homo sapiens) Explore Q8TBZ6  Go to UniProtKB:  Q8TBZ6
PHAROS:  Q8TBZ6 GTEx:  ENSG00000145331

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], O [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
EDO	D [auth A], P [auth B], Q [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	R [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
UNX	AA [auth B], BA [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	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: 0.243 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.097	α = 100.43
b = 43.309	β = 90.03
c = 60.347	γ = 92.88

Software Package:

Software Name	Purpose
CLS	data collection
SOLVE	phasing
RESOLVE	model building
BUSTER	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Dong, A., Zeng, H., Loppnau, P., Tempel, W., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary