9ARC

Crystal Structure of C0362 (TDE_0362 [TDE0362] resi 205-647)

PDB DOI: https://doi.org/10.2210/pdb9ARC/pdb

Classification: HYDROLASE
Organism(s): Treponema denticola
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-23 Released: 2024-11-27
Deposition Author(s): Clark, N.D., Malkowski, M.G.
Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.227
R-Value Work: 0.198
R-Value Observed: 0.199

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A dual domain bacterial virulence factor annihilates host innate immune defenses via degrading complement factors and blocking neutrophils chemotaxis

Kurniyati, K., Clark, N.D., Wang, H., Deng, Y., Sze, C.W., Visser, M.B., Balthasar, J.P., Malkowski, M.G., Li, C.

To be published.

Macromolecule Content

Total Structure Weight: 55.64 kDa
Atom Count: 3,877
Modelled Residue Count: 431
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial Ig-like domain protein C0362	A	476	Treponema denticola	Mutation(s): 0 Gene Names: TDE_0362
UniProt
Find proteins for Q73QT1 (Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104)) Explore Q73QT1 Go to UniProtKB: Q73QT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q73QT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

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: 1.77 Å
R-Value Free: 0.227
R-Value Work: 0.198
R-Value Observed: 0.199
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.598	α = 90
b = 99.258	β = 90
c = 121.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
cctbx.xfel	data reduction
Aimless	data scaling
DIALS	data reduction
xia2	data reduction
Blu-Ice	data collection

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Malkowski, M.G.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	5R01DE023080-10

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

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.