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.

Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7EZN

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of CnYvh1 complex with vanadate

Choi, M.K., Yoo, Y.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J9VTB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VO4 (Subject of Investigation/LOI) Query on VO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	VANADATE ION O₄ V LSGOVYNHVSXFFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.209 (Depositor), 0.209 (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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2022-06-08

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.