6NHI | pdb_00006nhi

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Models: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36nhi

Space Group: C 1 2 1

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

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• 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