6DM4 | pdb_00006dm4

Crystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila in complex with Homo sapiens Shc1 phospho-Tyr317 peptide

• PDB DOI: https://doi.org/10.2210/pdb6DM4/pdb

• Classification: PROTEIN BINDING
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1, Homo sapiens
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of the SH2 domain from RavO (Lpg1129) from Legionella pneumophila in complex with Homo sapiens Shc1 phospho-Tyr317 peptide

Kaneko, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.3 kDa 
• Atom Count: 4,528 
• Modeled Residue Count: 496 
• Deposited Residue Count: 501 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RavO	A, C [auth B], D [auth C], F [auth D]	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Shc1 phospho-Tyr317 peptide	B [auth E], E [auth G], G [auth H]	7	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P29353 (Homo sapiens) Explore P29353  Go to UniProtKB:  P29353
PHAROS:  P29353 GTEx:  ENSG00000160691

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], I [auth A], J [auth B], K [auth B], L [auth C], M [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B [auth E], E [auth G], G [auth H]	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.230 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.454	α = 72.6
b = 45.035	β = 90.14
c = 74.748	γ = 77.55

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 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)

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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  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary