4ZNG | pdb_00004zng

X-ray crystallography of recombinant Lactococcus lactis prolidase

• PDB DOI: https://doi.org/10.2210/pdb4ZNG/pdb

• Classification: HYDROLASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-04 Released: 2016-08-10 
• Deposition Author(s): Kgosisejo, O., Grochulski, P., Tanaka, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallography of recombinant Lactococcus lactis prolidase

Kgosisejo, O., Grochulski, P., Tanaka, T.

To be published.

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: 120.68 kDa 
• Atom Count: 8,636 
• Modeled Residue Count: 1,074 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolidase	A [auth C], B, C [auth A]	362	Lactococcus lactis	Mutation(s): 0  Gene Names: pepQ EC: 3.4.13.9
UniProt
Find proteins for A8WBX8 (Lactococcus lactis) Explore A8WBX8  Go to UniProtKB:  A8WBX8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	E [auth B], J [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth C], F [auth B], G [auth B], H [auth A], I [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.13	α = 90
b = 76.99	β = 112.39
c = 88.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Kgosisejo, O., Grochulski, P., Tanaka, T.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description