5W25 | pdb_00005w25

Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed with L-Aspartic Acid

• PDB DOI: https://doi.org/10.2210/pdb5W25/pdb

• Classification: LIGASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-05 Released: 2017-06-14 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Aspartyl-tRNA synthetase from Mycobacterium tuberculosis complexed with L-Aspartic Acid

Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.88 kDa 
• Atom Count: 8,317 
• Modeled Residue Count: 1,149 
• Deposited Residue Count: 1,232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate--tRNA(Asp/Asn) ligase	A, B	616	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: aspS, Rv2572c, MTCY227.29 EC: 6.1.1.23
UniProt
Find proteins for P9WFW3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFW3  Go to UniProtKB:  P9WFW3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LYS	D [auth A], E [auth A], H [auth B]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
GLU	F [auth A], I [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
ASP	C [auth A], G [auth B]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35W25

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.72	α = 90
b = 158.24	β = 93.77
c = 75.74	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-06-14
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-03-13
  Changes: Source and taxonomy