6DM3 | pdb_00006dm3

Crystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila, apoprotein

PDB DOI: https://doi.org/10.2210/pdb6DM3/pdb

Classification: PROTEIN BINDING
Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-06-04 Released: 2018-06-27
Deposition Author(s): Stogios, P.J., Evdokimova, E., Di Leo, R., Kaneko, T., Li, S., Savchenko, A., Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.318 (Depositor), 0.320 (DCC)
R-Value Work:
0.261 (Depositor), 0.260 (DCC)
R-Value Observed:
0.264 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila, apoprotein

Kaneko, T.

To be published.

Macromolecule Content

Total Structure Weight: 27.53 kDa
Atom Count: 1,821
Modeled Residue Count: 216
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RavO	A, B	120	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0 Gene Names: lpg1129
UniProt
Find proteins for Q5ZWF6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZWF6 Go to UniProtKB: Q5ZWF6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5ZWF6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.318 (Depositor), 0.320 (DCC)
R-Value Work: 0.261 (Depositor), 0.260 (DCC)
R-Value Observed: 0.264 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.037	α = 90
b = 72.981	β = 109.89
c = 71.961	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM074942
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History (Full details and data files)

Version 1.0: 2018-06-27
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2024-03-13
Changes: Data collection, Database references

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.