4WL8 | pdb_00004wl8

Crystal Structure of Mtb PEPCK in complex with non-hydrolyzable analog of GTP

• PDB DOI: https://doi.org/10.2210/pdb4WL8/pdb

• Classification: LYASE,TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-06 Released: 2015-10-21 
• Deposition Author(s): Kim, H.L., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Mtb PEPCK in complex with non-hydrolyzable analog of GTP

Kim, H.L.

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: 69.72 kDa 
• Atom Count: 5,613 
• Modeled Residue Count: 599 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.616	α = 90
b = 123.009	β = 116.97
c = 64.035	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-21 
Deposition Author(s): Kim, H.L., Sacchettini, J.C.

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description