8WV2 | pdb_00008wv2

Crystal structure of urethanase from Candida parapsilosis and structure-based Engineering to improve the catalytic activity and stability

• PDB DOI: https://doi.org/10.2210/pdb8WV2/pdb

• Classification: HYDROLASE
• Organism(s): Candida parapsilosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-10-22 Released: 2024-10-23 
• Deposition Author(s): Zhao, T., Wu, H.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of urethanase from Candida parapsilosis and structure-based Engineering to improve the catalytic activity and stability

Zhao, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 8-mer - A8 

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

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

Macromolecule Content 

• Total Structure Weight: 494.46 kDa 
• Atom Count: 35,789 
• Modeled Residue Count: 4,408 
• Deposited Residue Count: 4,408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidase family protein	A, B, C, D [auth E], E [auth F], F [auth G], G [auth H], H [auth D]	551	Candida parapsilosis	Mutation(s): 0  Gene Names: FOB60_005225
UniProt
Find proteins for A0A679EIJ6 (Candida parapsilosis) Explore A0A679EIJ6  Go to UniProtKB:  A0A679EIJ6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.42	α = 75.84
b = 110.158	β = 83.62
c = 180.584	γ = 73.95

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Zhao, T., Wu, H.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release