3SGI | pdb_00003sgi

Crystal structure of DNA ligase A BRCT domain deleted mutant of Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb3SGI/pdb

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


• Deposited: 2011-06-15 Released: 2012-06-20 
• Deposition Author(s): Kukshal, V., Ravishankar, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.322 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.311 (Depositor), 0.310 (DCC) 
• R-Value Observed: 
  0.312 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Domain deleted mutant of Mycobacterium tuberculosis NAD+ dependent DNA ligase capture the AMP cofactor in a new state

Kukshal, V., Ravishankar, R.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 68.09 kDa 
• Atom Count: 3,221 
• Modeled Residue Count: 408 
• Deposited Residue Count: 615 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A	615	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: lig, ligA, MT3094, MTV012.28c, Rv3014c EC: 6.5.1.2
UniProt
Find proteins for P9WNV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNV1  Go to UniProtKB:  P9WNV1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	B [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.322 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.311 (Depositor), 0.310 (DCC) 
• R-Value Observed: 0.312 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.437	α = 90
b = 99.564	β = 90
c = 144.009	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Kukshal, V., Ravishankar, R.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary