7L36

PEPCK steady-state structure with Mn and GTP

• PDB DOI: https://doi.org/10.2210/pdb7L36/pdb

• Classification: LYASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-17 Released: 2021-10-13 
• Deposition Author(s): Clinger, J.A., Moreau, D.W., McLeod, M.J., Holyoak, T., Thorne, R.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.199 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 

Literature

Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection.

Clinger, J.A., Moreau, D.W., McLeod, M.J., Holyoak, T., Thorne, R.E.

(2021) IUCrJ 8: 784-792

• PubMed: 34584739 
• DOI: https://doi.org/10.1107/S2052252521007053
• Primary Citation of Related Structures:  
  7L36, 7L3M, 7L3V


• PubMed Abstract: 
  

  Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and the complex experimental infrastructure that are required remain serious obstacles to its widespread application. Here, millisecond mix-and-quench crystallography (MMQX) has been developed, which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxy-kinase (PEPCK) is observed with a time resolution of 40 ms. By lowering the entry barrier to time-resolved crystallography, MMQX should enable a broad expansion in structural studies of protein dynamics.

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Organizational Affiliation: 

Physics Department, Cornell University, 142 Sciences Drive, Ithaca, NY 14853, USA.

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: 70.37 kDa 
• Atom Count: 5,304 
• Modelled Residue Count: 613 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]	A	624	Rattus norvegicus	Mutation(s): 0  Gene Names: Pck1 EC: 4.1.1.32 (PDB Primary Data), 2.7.11 (PDB Primary Data)
UniProt
Find proteins for P07379 (Rattus norvegicus) Explore P07379  Go to UniProtKB:  P07379

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	D [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MN	B [auth A], C [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.199 
• R-Value Work: 0.152 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.38	α = 90
b = 118.55	β = 109.53
c = 60.233	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-13 
Deposition Author(s): Clinger, J.A., Moreau, D.W., McLeod, M.J., Holyoak, T., Thorne, R.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM127528-01
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2021-10-13
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description