7SH3

Crystal Structure of a VirB8-like Protein of Type IV Secretion System from Rickettsia typhi in Complex with a Synthetic VirB8 Miniprotein Binder

PDB DOI: https://doi.org/10.2210/pdb7SH3/pdb

Classification: PROTEIN TRANSPORT
Organism(s): synthetic construct, Rickettsia typhi str. Wilmington
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-07 Released: 2021-10-20
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.306
R-Value Work: 0.238
R-Value Observed: 0.245

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a VirB8-like Protein of Type IV Secretion System from Rickettsia typhi in Complex with a Synthetic VirB8 Miniprotein Binder

DeBouver, N.D., Bera, A.K., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 28.82 kDa
Atom Count: 1,533
Modelled Residue Count: 188
Deposited Residue Count: 248
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic VirB8 Miniprotein Binder	A	67	synthetic construct	Mutation(s): 0 Gene Names: synthetic
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
VirB8-like protein of type IV secretion system	B	181	Rickettsia typhi str. Wilmington	Mutation(s): 0 Gene Names: RT0278
UniProt
Find proteins for Q68X84 (Rickettsia typhi (strain ATCC VR-144 / Wilmington)) Explore Q68X84 Go to UniProtKB: Q68X84
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68X84
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.306
R-Value Work: 0.238
R-Value Observed: 0.245
Space Group: I 2₁ 2₁ 2₁
Diffraction Data: https://doi.org/10.18430/m37sh3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.26	α = 90
b = 71.48	β = 90
c = 155.11	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.