2OO3

Crystal structure of protein LPL1258 from Legionella pneumophila str. Philadelphia 1, Pfam DUF519

• PDB DOI: https://doi.org/10.2210/pdb2OO3/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Legionella pneumophila subsp. pneumophila
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-25 Released: 2007-02-06 
• Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Slocombe, A., Reyes, C., Ozyurt, S., Smyth, L., Atwell, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.210 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Crystal structure of the hypothetical lpl1258 protein from Legionella pneumophila

Bonanno, J.B., Freeman, J., Bain, K.T., Slocombe, A., Reyes, C., Ozyurt, S., Smyth, L., Atwell, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.26 kDa 
• Atom Count: 2,381 
• Modelled Residue Count: 267 
• Deposited Residue Count: 283 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein involved in catabolism of external DNA	A	283	Legionella pneumophila subsp. pneumophila	Mutation(s): 0  Gene Names: lpl1258, lpg1296, DSM 7513
UniProt
Find proteins for Q5ZVZ2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZVZ2  Go to UniProtKB:  Q5ZVZ2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.210 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.822	α = 90
b = 72.959	β = 90
c = 78.379	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Bonanno, J.B., Freeman, J., Bain, K.T., Slocombe, A., Reyes, C., Ozyurt, S., Smyth, L., Atwell, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references