7KD3

Structure of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291

PDB DOI: https://doi.org/10.2210/pdb7KD3/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Clostridioides difficile R20291
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-07 Released: 2021-09-15
Deposition Author(s): Menon, S.K., Isom, C.E., Karr, E.A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258
R-Value Work: 0.200
R-Value Observed: 0.206

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291

Menon, S.K., Isom, C.E., West, A.H., Richter-Addo, G.B., Karr, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 26.41 kDa
Atom Count: 1,587
Modelled Residue Count: 197
Deposited Residue Count: 228
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A	114	Clostridioides difficile R20291	Mutation(s): 0 Gene Names: CDR20291_3200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	B	114	Clostridioides difficile R20291	Mutation(s): 0 Gene Names: CDR20291_3200
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258
R-Value Work: 0.200
R-Value Observed: 0.206
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.019	α = 90
b = 55.001	β = 96.06
c = 72.317	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-09-15
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection

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 R01GM133198.