6NHI

Crystal structure of Histidine--tRNA ligase from Elizabethkingia sp. CCUG 26117

PDB DOI: https://doi.org/10.2210/pdb6NHI/pdb

Classification: LIGASE
Organism(s): Elizabethkingia meningoseptica
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-12-21 Released: 2019-01-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.225
R-Value Work: 0.171
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Histidine--tRNA ligase from Elizabethkingia sp. CCUG 26117

Abendroth, J., Dranow, D.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 52 kDa
Atom Count: 3,723
Modelled Residue Count: 448
Deposited Residue Count: 457
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine--tRNA ligase	A	457	Elizabethkingia meningoseptica	Mutation(s): 0 Gene Names: hisS, NCTC10588_00401 EC: 6.1.1.21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.225
R-Value Work: 0.171
R-Value Observed: 0.174
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/m36nhi

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.8	α = 90
b = 68.56	β = 118.66
c = 97.22	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references
Version 1.2: 2024-04-03
Changes: 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 R01GM133198.