9VKF | pdb_00009vkf

Crystal structure of yeast arginine N-methyltransferase 1,HMT1

• PDB DOI: https://doi.org/10.2210/pdb9VKF/pdb

• Classification: GENE REGULATION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-23 Released: 2025-07-09 
• Deposition Author(s): Yang, X.Y., Zhou, Y.H., Shang, X.C., Liu, Y.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of yeast arginine N-methyltransferase 1,HMT1

Liu, Y.L., Yang, X.Y., Zhou, Y.H., Shang, X.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.36 kDa 
• Atom Count: 4,642 
• Modeled Residue Count: 579 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 1	A, B	328	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HMT1, ODP1, RMT1, YBR034C, YBR0320 EC: 2.1.1.319
UniProt
Find proteins for P38074 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38074  Go to UniProtKB:  P38074

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.67	α = 90
b = 84.67	β = 90
c = 97.72	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Yang, X.Y., Zhou, Y.H., Shang, X.C., Liu, Y.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271309

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release