8DHI | pdb_00008dhi

Crystal Structure of Clostridioides difficile Protein Tyrosine Phosphatase at pH 8.5

PDB DOI: https://doi.org/10.2210/pdb8DHI/pdb

Classification: HYDROLASE
Organism(s): Clostridioides difficile 6050
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-27 Released: 2023-07-05
Deposition Author(s): Lountos, G.T., Tropea, J.E.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.204 (Depositor), 0.205 (DCC)
R-Value Work:
0.174 (Depositor), 0.176 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Clostridioides difficile Protein Tyrosine Phosphatase at pH 8.5

Lountos, G.T., Tropea, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 57.94 kDa
Atom Count: 4,597
Modeled Residue Count: 478
Deposited Residue Count: 498
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYR_PHOSPHATASE_2 domain-containing protein	A, B	249	Clostridioides difficile 6050	Mutation(s): 0
UniProt
Find proteins for Q185E4 (Clostridioides difficile (strain 630)) Explore Q185E4 Go to UniProtKB: Q185E4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q185E4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.204 (Depositor), 0.205 (DCC)
R-Value Work: 0.174 (Depositor), 0.176 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.25	α = 90
b = 42.736	β = 106.53
c = 86.859	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description

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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.