3C9F | pdb_00003c9f

Crystal structure of 5'-nucleotidase from Candida albicans SC5314

• PDB DOI: https://doi.org/10.2210/pdb3C9F/pdb

• Classification: HYDROLASE
• Organism(s): Candida albicans SC5314
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-02-15 Released: 2008-02-26 
• Deposition Author(s): Patskovsky, Y., Romero, R., Gilmore, M., Eberle, M., Bain, K., Smith, D., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Crystal structure of 5'-nucleotidase from Candida albicans.

Patskovsky, Y., Romero, R., Gilmore, M., Eberle, M., Bain, K., Smith, D., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 129.29 kDa 
• Atom Count: 9,842 
• Modeled Residue Count: 1,071 
• Deposited Residue Count: 1,114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-nucleotidase	A, B	557	Candida albicans SC5314	Mutation(s): 6  Gene Names: USHA, CaO19.12802, CaO19.5342
UniProt
Find proteins for Q5A5Q7 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore Q5A5Q7  Go to UniProtKB:  Q5A5Q7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	E [auth A], J [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	D [auth A], G [auth B], H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.946	α = 90
b = 106.74	β = 90
c = 150.656	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Patskovsky, Y., Romero, R., Gilmore, M., Eberle, M., Bain, K., Smith, D., Wasserman, S.R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2024-02-21
  Changes: Data collection, Refinement description