4WIE

Crystal structure of apo-PEPCK from Mycobacterium tuberculosis with glycerol

• PDB DOI: https://doi.org/10.2210/pdb4WIE/pdb

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


• Deposited: 2014-09-25 Released: 2014-10-22 
• Deposition Author(s): Kim, H.L., Sacchettini, J.C.
• 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: 2.18 Å
• R-Value Free: 0.191 
• R-Value Work: 0.138 
• R-Value Observed: 0.141 

Literature

Crystal structure of apo-PEPCK from Mycobacterium tuberculosis with glycerol

Kim, H.L., Sacchettini, J.C.

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: 69.19 kDa 
• Atom Count: 5,409 
• Modelled Residue Count: 600 
• Deposited Residue Count: 622 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase [GTP]	A	622	Mycobacterium tuberculosis H37Ra	Mutation(s): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.191 
• R-Value Work: 0.138 
• R-Value Observed: 0.141 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.958	α = 90
b = 122.564	β = 117
c = 64.555	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	phasing
PHENIX	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Kim, H.L., Sacchettini, J.C.

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

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Other
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description