2EL9

Crystal structure of E.coli Histidyl-tRNA synthetase complexed with a histidyl-adenylate analogue

• PDB DOI: https://doi.org/10.2210/pdb2EL9/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-27 Released: 2008-03-18 
• Deposition Author(s): Yanagisawa, T., Si, S.Y., Matsuno, M., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.285 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

Crystal structure of E.coli Histidyl-tRNA synthetase complexed with a histidyl-adenylate analogue

Yanagisawa, T., Si, S.Y., Matsuno, M., Ishii, R., Yokoyama, S.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 193.13 kDa 
• Atom Count: 12,050 
• Modelled Residue Count: 1,505 
• Deposited Residue Count: 1,724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidyl-tRNA synthetase	A, B, C, D	431	Escherichia coli	Mutation(s): 0  Gene Names: hisS EC: 6.1.1.21
UniProt
Find proteins for P60906 (Escherichia coli (strain K12)) Explore P60906  Go to UniProtKB:  P60906

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HSS	E [auth A], F [auth B], G [auth C], H [auth D]	5'-O-[(L-HISTIDYLAMINO)SULFONYL]ADENOSINE C16 H21 N9 O7 S WRXPXUSZYDNAQP-LEJQEAHTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.285 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.113	α = 90
b = 108.345	β = 98.21
c = 193.645	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Yanagisawa, T., Si, S.Y., Matsuno, M., Ishii, R., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description