2BDE | pdb_00002bde

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

• PDB DOI: https://doi.org/10.2210/pdb2BDE/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-20 Released: 2005-12-06 
• Deposition Author(s): Forouhar, F., Abashidze, M., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.267 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

Crystal Structure of the cytosolic IMP-GMP specific 5'-nucleotidase (lpg0095) from Legionella pneumophila, Northeast Structural Genomics Target LgR1

Forouhar, F., Abashidze, M., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 55.35 kDa 
• Atom Count: 3,839 
• Modeled Residue Count: 458 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cytosolic IMP-GMP specific 5'-nucleotidase	A	470	Legionella pneumophila	Mutation(s): 9  Gene Names: 3078646
UniProt
Find proteins for Q5ZZB6 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZB6  Go to UniProtKB:  Q5ZZB6

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.267 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.54	α = 90
b = 152.54	β = 90
c = 188.406	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Forouhar, F., Abashidze, M., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary