3DJC

CRYSTAL STRUCTURE OF PANTOTHENATE KINASE FROM LEGIONELLA PNEUMOPHILA

• PDB DOI: https://doi.org/10.2210/pdb3DJC/pdb

• Classification: TRANSFERASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Mutation(s): No 


• Deposited: 2008-06-23 Released: 2008-07-15 
• Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Romero, R., Dickey, M., Logan, C., Wasserman, S., Maletic, M., Koss, J., 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: 2.40 Å
• R-Value Free: 0.313 
• R-Value Work: 0.259 
• R-Value Observed: 0.261 

Literature

Crystal Structure of Pantothenate Kinase from Legionella Pneumophila

Patskovsky, Y., Bonanno, J.B., Romero, R., Dickey, M., Logan, C., Maletic, M., Wasserman, S., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 348.91 kDa 
• Atom Count: 23,826 
• Modelled Residue Count: 3,040 
• Deposited Residue Count: 3,192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III pantothenate kinase	A, B, C, D, E, F, G, H, I, J, K, L	266	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: coaX, lpg0911 EC: 2.7.1.33
UniProt
Find proteins for Q5ZX22 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZX22  Go to UniProtKB:  Q5ZX22

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	M [auth A], N [auth A], O [auth B], P [auth C], Q [auth C], R [auth E], S [auth E], T [auth H], U [auth H], V [auth J], W [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.313 
• R-Value Work: 0.259 
• R-Value Observed: 0.261 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.394	α = 90
b = 134.571	β = 93.24
c = 134.404	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Patskovsky, Y., Bonanno, J.B., Romero, R., Dickey, M., Logan, C., Wasserman, S., Maletic, M., Koss, J., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2012-10-24
  Changes: Structure summary
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references