2PY7 | pdb_00002py7

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+

• PDB DOI: https://doi.org/10.2210/pdb2PY7/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2007-05-15 Released: 2008-04-22 
• Deposition Author(s): Delbaere, L.T.J., Cotelesage, J.J.H., Goldie, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.218 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser

Delbaere, L.T.J., Cotelesage, J.J.H., Goldie, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.31 kDa 
• Atom Count: 4,737 
• Modeled Residue Count: 535 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase	A [auth X]	540	Escherichia coli K-12	Mutation(s): 1  Gene Names: pckA EC: 4.1.1.49
UniProt
Find proteins for P22259 (Escherichia coli (strain K12)) Explore P22259  Go to UniProtKB:  P22259

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth X]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MN	C [auth X], D [auth X]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	B [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.218 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.999	α = 90
b = 95.663	β = 96.12
c = 46.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Delbaere, L.T.J., Cotelesage, J.J.H., Goldie, H.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description