6BYQ | pdb_00006byq

Crystal structure of Tyrosine-tRNA ligase from Helicobacter pylori G27

PDB DOI: https://doi.org/10.2210/pdb6BYQ/pdb

Classification: LIGASE
Organism(s): Helicobacter pylori G27
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-12-21 Released: 2018-03-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Tyrosine-tRNA ligase from Helicobacter pylori G27

Abendroth, J., Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 46.79 kDa
Atom Count: 2,507
Modeled Residue Count: 313
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase	A	410	Helicobacter pylori G27	Mutation(s): 0 Gene Names: tyrS, HPG27_731 EC: 6.1.1.1
UniProt
Find proteins for B5Z7D7 (Helicobacter pylori (strain G27)) Explore B5Z7D7 Go to UniProtKB: B5Z7D7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5Z7D7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-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: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data: https://doi.org/10.18430/M36BYQ

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.4	α = 90
b = 43.36	β = 121.21
c = 113.7	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building
SIMBAD	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.