7L3M

PEPCK MMQX structure 40ms post-mixing with oxaloacetic acid

PDB DOI: https://doi.org/10.2210/pdb7L3M/pdb

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

Deposited: 2020-12-18 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.186
R-Value Work: 0.172
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 70.49 kDa
Atom Count: 5,234
Modelled Residue Count: 612
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07379
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PEP (Subject of Investigation/LOI) Query on PEP Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PHOSPHOENOLPYRUVATE C₃ H₅ O₆ P DTBNBXWJWCWCIK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain B [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	B [auth A], G [auth A], H [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain G [auth A] Focus chain H [auth A]
CO2 Query on CO2 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CARBON DIOXIDE C O₂ CURLTUGMZLYLDI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
PEP	BindingDB: 7L3M	Ki: 2.89e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.186
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.389	α = 90
b = 118.935	β = 109.421
c = 60.3	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-13

Deposition Author(s):

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	--