5CCA | pdb_00005cca

Crystal structure of Mtb toxin

• PDB DOI: https://doi.org/10.2210/pdb5CCA/pdb

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


• Deposited: 2015-07-01 Released: 2016-09-07 
• Deposition Author(s): Cascio, D., Arbing, M., de Serrano, V., Eisenberg, D., Miallau, L., TB Structural Genomics Consortium (TBSGC)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.302 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.300 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.300 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Mtb toxin

Cascio, D., Arbing, M., de Serrano, V., Eisenberg, D., Miallau, L., TB Structural Genomics Consortium (TBSGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.03 kDa 
• Atom Count: 1,379 
• Modeled Residue Count: 185 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease MazF3	A, B	124	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: mazF3, MT1134 EC: 3.1
UniProt
Find proteins for P9WIH9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIH9  Go to UniProtKB:  P9WIH9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.302 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.300 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.300 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.555	α = 90
b = 105.555	β = 90
c = 142.417	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
REFMAC	refinement
HKL-2000	data reduction
MR-Rosetta	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Cascio, D., Arbing, M., de Serrano, V., Eisenberg, D., Miallau, L., TB Structural Genomics Consortium (TBSGC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	99-S150606
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	PO1AIO68135

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Advisory, Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary