7EZN | pdb_00007ezn

Crystal structure of CnYvh1 complex with vanadate

• PDB DOI: https://doi.org/10.2210/pdb7EZN/pdb

• Classification: HYDROLASE
• Organism(s): Cryptococcus neoformans H99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-06-01 Released: 2022-06-08 
• Deposition Author(s): Choi, M.K., Yoo, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CnYvh1 complex with vanadate

Choi, M.K., Yoo, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.93 kDa 
• Atom Count: 1,455 
• Modeled Residue Count: 175 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-tyrosine-phosphatase	A	205	Cryptococcus neoformans H99	Mutation(s): 0  Gene Names: CNAG_01203 EC: 3.1.3.48
UniProt
Find proteins for J9VTB5 (Cryptococcus neoformans (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VTB5  Go to UniProtKB:  J9VTB5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VO4 (Subject of Investigation/LOI)	B [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.194	α = 90
b = 66.194	β = 90
c = 120.324	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Choi, M.K., Yoo, Y.

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description