2HGZ

Crystal structure of a p-benzoyl-L-phenylalanyl-tRNA synthetase

PDB DOI: https://doi.org/10.2210/pdb2HGZ/pdb

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

Deposited: 2006-06-27 Released: 2007-06-05
Deposition Author(s): Liu, W., Alfonta, L., Mack, A.V., Schultz, P.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.270
R-Value Work: 0.210
R-Value Observed: 0.217

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural basis for the recognition of para-benzoyl-L-phenylalanine by evolved aminoacyl-tRNA synthetases.

Liu, W., Alfonta, L., Mack, A.V., Schultz, P.G.

(2007) Angew Chem Int Ed Engl 46: 6073-6075

PubMed: 17628477 Search on PubMed
DOI: https://doi.org/10.1002/anie.200701990
Primary Citation of Related Structures:
2HGZ

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: 35.2 kDa
Atom Count: 2,602
Modelled Residue Count: 306
Deposited Residue Count: 306
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	306	Methanocaldococcus jannaschii	Mutation(s): 3 Gene Names: tyrS 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
PBF Query on PBF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PARA-(BENZOYL)-PHENYLALANINE C₁₆ H₁₅ N O₃ TVIDEEHSOPHZBR-AWEZNQCLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.270
R-Value Work: 0.210
R-Value Observed: 0.217
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.639	α = 90
b = 101.639	β = 90
c = 71.466	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2008-02-06
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2024-02-14
Changes: Data collection
Version 1.5: 2024-04-03
Changes: Refinement description