3ZXI | pdb_00003zxi

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with a tyrosyl-adenylate analog

PDB DOI: https://doi.org/10.2210/pdb3ZXI/pdb

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

Deposited: 2011-08-11 Released: 2011-11-16
Deposition Author(s): Bonnefond, L., Frugier, M., Rudinger-Thirion, J., Balg, C., Chenevert, R., Lorber, B., Giege, R., Sauter, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.307 (Depositor), 0.308 (DCC)
R-Value Work:
0.224 (Depositor), 0.223 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Exploiting Protein Engineering and Crystal Polymorphism for Successful X-Ray Structure Determination

Bonnefond, L., Schellenberger, P., Basquin, J., Demangeat, G., Ritzenthaler, C., Chenevert, R., Balg, C., Frugier, M., Rudinger-Thirion, J., Giege, R., Lorber, B., Sauter, C.

(2011) Cryst Growth Des 11: 4334

DOI: https://doi.org/10.1021/CG101468P

Macromolecule Content

Total Structure Weight: 80.92 kDa
Atom Count: 4,928
Modeled Residue Count: 612
Deposited Residue Count: 712
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSYL-TRNA SYNTHETASE, MITOCHONDRIAL	A, B	356	Homo sapiens	Mutation(s): 0 EC: 6.1.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Z4 (Homo sapiens) Explore Q9Y2Z4 Go to UniProtKB: Q9Y2Z4
PHAROS: Q9Y2Z4 GTEx: ENSG00000139131
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2Z4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TYA Query on TYA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PHOSPHORIC ACID 2-AMINO-3-(4-HYDROXY-PHENYL)-PROPYL ESTER ADENOSIN-5'YL ESTER C₁₉ H₂₄ N₆ O₈ P JJLCVHBFTXDJMM-KFAHYOAQSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.307 (Depositor), 0.308 (DCC)
R-Value Work: 0.224 (Depositor), 0.223 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.14	α = 90
b = 62.87	β = 90
c = 196.32	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-16
Type: Initial release
Version 1.1: 2019-03-06
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description