8J6V | pdb_00008j6v

Structure of yeast Arginyl-tRNA-protein transferase 1

PDB DOI: https://doi.org/10.2210/pdb8J6V/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-26 Released: 2023-06-07
Deposition Author(s): Yashiro, Y., Tomita, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.238 (Depositor), 0.240 (DCC)
R-Value Observed:
0.240 (Depositor)

Starting Model: in silico
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This is version 1.1 of the entry. See complete history.

Literature

Structure of Arginyl-tRNA-protein transferase 1

Yashiro, Y., Tomita, T.

To be published.

Macromolecule Content

Total Structure Weight: 708.87 kDa
Atom Count: 45,256
Modeled Residue Count: 5,575
Deposited Residue Count: 6,132
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
arginyltransferase	A B C [auth D] D [auth F] E A, B, C [auth D], D [auth F], E, F [auth L], G [auth H], H [auth G], I [auth C], J [auth K], K [auth I], L [auth J]	511	Saccharomyces cerevisiae	Mutation(s): 3 Gene Names: ATE1 EC: 2.3.2.8
UniProt
Find proteins for P16639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16639 Go to UniProtKB: P16639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16639
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.270 (Depositor), 0.270 (DCC)
R-Value Work: 0.238 (Depositor), 0.240 (DCC)
R-Value Observed: 0.240 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 235.66	α = 90
b = 235.66	β = 90
c = 171.57	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	LS136
Japan Society for the Promotion of Science (JSPS)	Japan	18H03980
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	26113002
Japan Society for the Promotion of Science (JSPS)	Japan	19K16069
Japan Society for the Promotion of Science (JSPS)	Japan	23H00368
Japan Society for the Promotion of Science (JSPS)	Japan	22K15055

Revision History (Full details and data files)

Version 1.0: 2023-06-07
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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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.