5YM9 | pdb_00005ym9

Crystal Structure of the Deamidase from Legionella pneumophila

• PDB DOI: https://doi.org/10.2210/pdb5YM9/pdb

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


• Deposited: 2017-10-21 Released: 2018-10-24 
• Deposition Author(s): Zhu, Z.L., Zhu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal Structure of the Deamidase from Legionella pneumophila

Zhu, Z.L., Zhu, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.09 kDa 
• Atom Count: 6,405 
• Modeled Residue Count: 768 
• Deposited Residue Count: 768 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	384	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: lpg2148
UniProt
Find proteins for Q5ZTL3 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZTL3  Go to UniProtKB:  Q5ZTL3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.101	α = 90
b = 135.895	β = 90
c = 64.578	γ = 90

Software Package:

Software Name	Purpose
DENZO	data collection
HKL-2000	data scaling
PHASES	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Zhu, Z.L., Zhu, M.

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references