7ZBR | pdb_00007zbr

Crystal Structure of full-length Bartonella Effector protein 1

PDB DOI: https://doi.org/10.2210/pdb7ZBR/pdb

Classification: TOXIN
Organism(s): Bartonella clarridgeiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-03-24 Released: 2023-04-05
Deposition Author(s): Huber, M.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.303 (Depositor), 0.300 (DCC)
R-Value Work:
0.270 (Depositor), 0.270 (DCC)
R-Value Observed:
0.273 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Full-length structure of a FIC effector protein from Bartonella reveals a novel structural domain

Huber, M., Wagner, A., Reiners, J., Seyfert, C.E.M., Smits, S.H.J., Schirmer, T., Dehio, C.

To be published.

Macromolecule Content

Total Structure Weight: 63.82 kDa
Atom Count: 4,196
Modeled Residue Count: 531
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bartonella effector protein (Bep) substrate of VirB T4SS	A	566	Bartonella clarridgeiae	Mutation(s): 0 Gene Names: BARCL_0069 EC: 2.7.7.108
UniProt
Find proteins for E6YFW2 (Bartonella clarridgeiae (strain CCUG 45776 / CIP 104772 / 73)) Explore E6YFW2 Go to UniProtKB: E6YFW2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E6YFW2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.303 (Depositor), 0.300 (DCC)
R-Value Work: 0.270 (Depositor), 0.270 (DCC)
R-Value Observed: 0.273 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.492	α = 90
b = 70.492	β = 90
c = 213.961	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2023-04-05
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

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.