4QN8 | pdb_00004qn8

The crystal structure of an effector protein VipE from Legionella pneumophila subsp. pneumophila str. Philadelphia 1

PDB DOI: https://doi.org/10.2210/pdb4QN8/pdb

Classification: SIGNALING PROTEIN
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2014-06-17 Released: 2014-07-16
Deposition Author(s): Tan, K., Xu, X., Cui, H., Liu, S., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.233 (Depositor), 0.232 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4QN8

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

Literature

The crystal structure of an effector protein VipE from Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Tan, K., Xu, X., Cui, H., Liu, S., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 52.96 kDa
Atom Count: 3,945
Modeled Residue Count: 455
Deposited Residue Count: 465
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VipE	A, B, C	155	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: lpg2813, vipE
UniProt
Find proteins for Q5ZRR7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRR7 Go to UniProtKB: Q5ZRR7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5ZRR7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B]	D [auth A], E [auth A], F [auth B], G [auth C]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.233 (Depositor), 0.232 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.553	α = 90
b = 77.553	β = 90
c = 71.997	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.