Macromolecule Content

Total Structure Weight: 58.19 kDa
Atom Count: 4,291
Modelled Residue Count: 500
Deposited Residue Count: 502
Unique protein chains: 1

2D54

Crystal Structure of Methionyl tRNA Synthetase Y225A Mutant from Thermus Thermophilus

PDB DOI: https://doi.org/10.2210/pdb2D54/pdb

Classification: ISOMERASE
Organism(s): Thermus thermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-10-28 Released: 2006-12-19
Deposition Author(s): Konno, M., Takeda, R., Takasaka, R., Mori, Y., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.254
R-Value Work: 0.208

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Y225F/Amutation for Met-tRNA synthetase reveals importance of hydrophobic circumstance

Konno, M., Takeda, R., Takasaka, R., Mori, Y., Ishii, R., Yokoyama, S.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase	A	502	Thermus thermophilus	Mutation(s): 1 EC: 6.1.1.10
UniProt
Find proteins for P23395 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P23395 Go to UniProtKB: P23395
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23395
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.254
R-Value Work: 0.208
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.318	α = 90
b = 82.209	β = 90
c = 120.56	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2006-12-19
Type: Initial release
Version 1.1: 2007-10-09
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.