2PXH

Crystal structure of a bipyridylalanyl-tRNA synthetase

PDB DOI: https://doi.org/10.2210/pdb2PXH/pdb

Classification: LIGASE
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-05-14 Released: 2008-02-05
Deposition Author(s): Liu, W., Xie, J., Schultz, P.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.242
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

A genetically encoded bidentate, metal-binding amino acid.

Xie, J., Liu, W., Schultz, P.G.

(2007) Angew Chem Int Ed Engl 46: 9239-9242

PubMed: 17893898 Search on PubMed
DOI: https://doi.org/10.1002/anie.200703397
Primary Citation of Related Structures:
2PXH

Organizational Affiliation

Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 36.28 kDa
Atom Count: 2,748
Modelled Residue Count: 306
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-tRNA synthetase	A	314	Methanocaldococcus jannaschii	Mutation(s): 7 Gene Names: tyrosyl-tRNA synthetase EC: 6.1.1.1
UniProt
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57834 Go to UniProtKB: Q57834
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57834
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BP5 Query on BP5 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	3-(2,2'-BIPYRIDIN-5-YL)-L-ALANINE C₁₃ H₁₃ N₃ O₂ VWTQURBMIRJISI-JTQLQIEISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.242
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.841	α = 90
b = 100.841	β = 90
c = 71.072	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-02-05

Deposition Author(s):

Liu, W.

Xie, J.

Schultz, P.G.

Revision History (Full details and data files)

Version 1.0: 2008-02-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection