5E2C | pdb_00005e2c

Crystal structure of N-terminal domain of cytoplasmic peptidase PepQ from Mycobacterium tuberculosis H37Rv

• PDB DOI: https://doi.org/10.2210/pdb5E2C/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-30 Released: 2015-10-14 
• Deposition Author(s): Chang, C., Endres, L., Endres, M., SACCHETTINI, J., JOACHIMIAK, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.137 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Crystal structure of N-terminal domain of cytoplasmic peptidase PepQ from Mycobacterium tuberculosis H37Rv

Chang, C., Endres, L., Endres, M., SACCHETTINI, J., JOACHIMIAK, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.65 kDa 
• Atom Count: 2,400 
• Modeled Residue Count: 260 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Pro dipeptidase	A, B	132	Mycobacterium tuberculosis H37Ra	Mutation(s): 0  Gene Names: pepQ, MRA_2563
UniProt
Find proteins for A5U5N4 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5U5N4  Go to UniProtKB:  A5U5N4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.137 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.684	α = 90
b = 60.202	β = 90
c = 96.268	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing
SBC-Collect	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Chang, C., Endres, L., Endres, M., SACCHETTINI, J., JOACHIMIAK, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary