3VU8

Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue

PDB DOI: https://doi.org/10.2210/pdb3VU8/pdb

Classification: LIGASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-22 Released: 2013-06-26
Deposition Author(s): Konno, M., Kato-Murayama, M., Toma-Fukai, S., Uchikawa, E., Nureki, O., Yokoyama, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.300
R-Value Work: 0.200
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases

Konno, M., Kato-Murayama, M., Takeda, R., Takasaka, R., Uchikawa, E., Toma-Fukai, S., Ishii, R., Nureki, O., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 58.76 kDa
Atom Count: 4,263
Modelled Residue Count: 500
Deposited Residue Count: 502
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase	A	502	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: metS 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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MDS Query on MDS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	N-[METHIONYL]-N'-[ADENOSYL]-DIAMINOSULFONE C₁₅ H₂₄ N₈ O₆ S₂ DAUQVCLMADDCHF-QWRDWHBNSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.300
R-Value Work: 0.200
R-Value Observed: 0.205
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.823	α = 90
b = 82.682	β = 90
c = 120.165	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	model building
X-PLOR	refinement
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-06-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-26
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3VU8

Metionyl-tRNA synthetase from Thermus thermophilus complexed with methionyl-adenylate analogue

The modeling of structures of specific conformation of homosysteine-AMP leading to thiolactone-formation on class Ia aminoacyl-tRNA synthetases

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)