5TY0 | pdb_00005ty0

2.22 Angstrom Crystal Structure of N-terminal Fragment (residues 1-419) of Elongation Factor G from Legionella pneumophila.

• PDB DOI: https://doi.org/10.2210/pdb5TY0/pdb

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


• Deposited: 2016-11-17 Released: 2016-11-30 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Cardona-Correa, A., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc 14: e0020025-e0020025

• PubMed: 40391899 
• DOI: https://doi.org/10.1128/mra.00200-25
• Primary Citation of Related Structures:  
  5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V36, 5VDN, 5VFB, 5VH6, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, 6PXA, 6W2Z, 9BZN, 9BZQ


• PubMed Abstract: 
  

  Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

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Organizational Affiliation: 
• Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.
Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois, USA.
Biozone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Biosciences Division, University of California, Riverside, School of Medicine, Riverside, California, USA.
Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.23 kDa 
• Atom Count: 3,287 
• Modeled Residue Count: 378 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor G	A	422	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: fusA, lpg0326
UniProt
Find proteins for Q5ZYP6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZYP6  Go to UniProtKB:  Q5ZYP6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	C [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35ty0

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.399	α = 90
b = 89.853	β = 90
c = 117.98	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-30 
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Cardona-Correa, A., Dubrovska, I., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2026-02-11
  Changes: Database references, Structure summary