8HYR | pdb_00008hyr

Crystal structure of human KARS apo

PDB DOI: https://doi.org/10.2210/pdb8HYR/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia phage EcSzw-2
Mutation(s): No

Deposited: 2023-01-07 Released: 2024-07-10
Deposition Author(s): Zhang, X., Wang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.245 (Depositor), 0.250 (DCC)
R-Value Work:
0.215 (Depositor), 0.210 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human KARS apo

Zhang, X., Wang, Y., Ouyang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 120.39 kDa
Atom Count: 8,294
Modeled Residue Count: 999
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B	520	Homo sapiens	Mutation(s): 0 Gene Names: KARS1, KARS, KIAA0070 EC: 2.7.7 (PDB Primary Data), 6.1.1.6 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q15046 (Homo sapiens) Explore Q15046 Go to UniProtKB: Q15046
PHAROS: Q15046 GTEx: ENSG00000065427
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15046
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.245 (Depositor), 0.250 (DCC)
R-Value Work: 0.215 (Depositor), 0.210 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.331	α = 90
b = 107.664	β = 90
c = 130.516	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870751
Ministry of Science and Technology (MoST, China)	China	2018YFE0204500

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release

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.