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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.284 (Depositor), 0.285 (DCC)
R-Value Work:
0.235 (Depositor), 0.235 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38074
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.284 (Depositor), 0.285 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.