4H5Y | pdb_00004h5y

High-resolution crystal structure of Legionella pneumophila LidA (60-594)

• PDB DOI: https://doi.org/10.2210/pdb4H5Y/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-19 Released: 2013-09-25 
• Deposition Author(s): An, X., Ye, S., Liu, Y., Zheng, X., Zhang, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

The crystal structure of LidA, a translocated substrate of the Legionella pneumophila type IV secretion system.

Meng, G., An, X., Ye, S., Liu, Y., Zhu, W., Zhang, R., Zheng, X.

(2013) Protein Cell 4: 897-900

• PubMed: 24293259 
• DOI: https://doi.org/10.1007/s13238-013-2100-7
• Primary Citation Related Structures: 
  4H5Y

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Organizational Affiliation: 
• State Key Lab of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.

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: 65.48 kDa 
• Atom Count: 4,707 
• Modeled Residue Count: 528 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LidA protein, substrate of the Dot/Icm system	A	570	Legionella pneumophila	Mutation(s): 0  Gene Names: lidA, LPC_2349

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.554	α = 90
b = 64.468	β = 90
c = 164.373	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): An, X., Ye, S., Liu, Y., Zheng, X., Zhang, R.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references