5I67

Crystal Structure Analysis of MTB PEPCK mutant C273S

• PDB DOI: https://doi.org/10.2210/pdb5I67/pdb

• Classification: LYASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2016-02-16 Released: 2016-04-06 
• Deposition Author(s): Dostal, J., Pachl, P., Machova, I., Pichova, I., Snasel, J.
• Funding Organization(s): NPU, RVO

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Crystal Structure Analysis of MTB PEPCK mutant C273S

Dostal, J., Pachl, P., Machova, I., Pichova, I., Snasel, J.

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: 68.05 kDa 
• Atom Count: 4,667 
• Modelled Residue Count: 588 
• Deposited Residue Count: 605 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase [GTP]	A	605	Mycobacterium tuberculosis H37Ra	Mutation(s): 1  Gene Names: pckG, MRA_0219 EC: 4.1.1.32
UniProt
Find proteins for A5TYT6 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5TYT6  Go to UniProtKB:  A5TYT6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PEG	C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
MN	F [auth A], G [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.244 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.721	α = 90
b = 124.598	β = 90
c = 121.302	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Dostal, J., Pachl, P., Machova, I., Pichova, I., Snasel, J.

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Funding Organization	Location	Grant Number
NPU	Czech Republic	LO1302
NPU	Czech Republic	LO1304
RVO	Czech Republic	RVO 68378050
RVO	Czech Republic	RVO 631388963

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description