5E3I | pdb_00005e3i

Crystal Structure of a Histidyl-tRNA synthetase from Acinetobacter baumannii with bound L-Histidine and ATP

• PDB DOI: https://doi.org/10.2210/pdb5E3I/pdb

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


• Deposited: 2015-10-02 Released: 2015-11-04 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Histidyl-tRNA synthetase from Acinetobacter baumannii with bound L-Histidine and ATP

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Lukacs, C.M., Dranow, D.M., Lorimer, D., 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)

Macromolecule Content 

• Total Structure Weight: 100.32 kDa 
• Atom Count: 6,608 
• Modeled Residue Count: 786 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine--tRNA ligase	A, B	438	Acinetobacter baumannii	Mutation(s): 0  Gene Names: hisS, ABUW_3376, IOMTU433_3293, RU84_15845 EC: 6.1.1.21
UniProt
Find proteins for B0VKR7 (Acinetobacter baumannii (strain SDF)) Explore B0VKR7  Go to UniProtKB:  B0VKR7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
HIS	E [auth A], H [auth B]	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35E3I

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.81	α = 90
b = 103.07	β = 90
c = 246.3	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2025-10-22
  Changes: Database references, Structure summary