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), 0.238 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

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

Zhao, T.

To be published.

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

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amidase family protein	A B C D [auth E] E [auth F] 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A679EIJ6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.237 (Depositor), 0.238 (DCC)
R-Value Work: 0.204 (Depositor), 0.205 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.