5GOY | pdb_00005goy

The crystal structure of human cytosolic methionyl-tRNA synthetase in complex with methionine

PDB DOI: https://doi.org/10.2210/pdb5GOY/pdb

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

Deposited: 2016-07-30 Released: 2017-08-02
Deposition Author(s): Lee, H.J., Cho, H.Y., Kang, B.S.
Funding Organization(s): National Research Foundation of Korea

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

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

Literature

The crystal structure of human cytosolic methionyl-tRNA synthetase in complex with methionine

Lee, H.J., Cho, H.Y., Kang, B.S.

To be published.

Macromolecule Content

Total Structure Weight: 71.32 kDa
Atom Count: 5,022
Modeled Residue Count: 598
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase, cytoplasmic	A	624	Homo sapiens	Mutation(s): 0 Gene Names: MARS EC: 6.1.1.10
UniProt & NIH Common Fund Data Resources
Find proteins for P56192 (Homo sapiens) Explore P56192 Go to UniProtKB: P56192
PHAROS: P56192 GTEx: ENSG00000166986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56192
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MET Query on MET Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	METHIONINE C₅ H₁₁ N O₂ S FFEARJCKVFRZRR-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.539	α = 90
b = 93.133	β = 90
c = 122.482	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-08-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation of Korea	Korea, Republic Of	NRF-2015R1A4A1042271

Revision History (Full details and data files)

Version 1.0: 2017-08-02
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.