3LSS

Trypanosoma brucei seryl-tRNA synthetase in complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb3LSS/pdb

• Classification: LIGASE
• Organism(s): Trypanosoma brucei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-12 Released: 2010-03-02 
• Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

Starting Model: experimental

Literature

X-ray crystal structure of Seryl-tRNA synthetase from the eukaryotic parasite Trypanosoma brucei.

Larson, E.T., Zhang, L., Napuli, A., Mueller, N., Verlinde, C.L.M.J., Van Voorhis, W.C., Buckner, F.S., Fan, E., Hol, W.G.J., Merritt, E.A.

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: 109.95 kDa 
• Atom Count: 7,683 
• Modelled Residue Count: 906 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seryl-tRNA synthetase	A, B	484	Trypanosoma brucei	Mutation(s): 0  Gene Names: SerRS, Tb11.02.5020 EC: 6.1.1.11
UniProt
Find proteins for Q384V4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q384V4  Go to UniProtKB:  Q384V4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A], G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MLI	D [auth A], E [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.652	α = 90
b = 175.652	β = 90
c = 248.518	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description