5HK3 | pdb_00005hk3

Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb5HK3/pdb
• NAKB: 5HK3

• Classification: hydrolase/dna
• Organism(s): Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-01-13 Released: 2017-01-18 
• Deposition Author(s): Yen, T.J., Brennan, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: other

Literature

Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with DNA

Yen, T.J., Brennan, R.G.

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: 27.72 kDa 
• Atom Count: 1,913 
• Modeled Residue Count: 221 
• Deposited Residue Count: 239 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF6	A, B	114	Mycobacterium tuberculosis H37Rv	Mutation(s): 2  Gene Names: mazF6, mazF-mt3, Rv1991c, MTCY39.28 EC: 3.1.27
UniProt
Find proteins for P9WII3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WII3  Go to UniProtKB:  P9WII3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*UP*CP*UP*CP*CP*UP*UP*UP*C)-3')	C	11	Mycobacterium tuberculosis

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.311	α = 90
b = 64.244	β = 90
c = 73.915	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Yen, T.J., Brennan, R.G.

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-04-03
  Changes: Refinement description