7E5C

Bacterial prolidase mutant D45W/L225Y/H226L/H343I

• PDB DOI: https://doi.org/10.2210/pdb7E5C/pdb

• Classification: HYDROLASE
• Organism(s): Pseudoalteromonas lipolytica SCSIO 04301
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-02-18 Released: 2021-03-03 
• Deposition Author(s): Yang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Structure-based redesign of the bacterial prolidase active-site pocket for efficient enhancement of methyl-parathion hydrolysis

Yang, J., Xiao, Y., Liu, Y., Li, R., Long, L.

(2021) Catal Sci Technol 11: 5086-5093

• DOI: https://doi.org/10.1039/d1cy00490e

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 207.34 kDa 
• Atom Count: 14,635 
• Modelled Residue Count: 1,755 
• Deposited Residue Count: 1,792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Pro dipeptidase	A, B, C, D	448	Pseudoalteromonas lipolytica SCSIO 04301	Mutation(s): 4  Gene Names: pepQ EC: 3.4.13.9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.965	α = 90
b = 182.965	β = 90
c = 372.079	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Yang, J.

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-08-18
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description