3D0K

Crystal structure of the LpqC, poly(3-hydroxybutyrate) depolymerase from Bordetella parapertussis

• PDB DOI: https://doi.org/10.2210/pdb3D0K/pdb

• Classification: HYDROLASE
• Mutation(s): No 


• Deposited: 2008-05-01 Released: 2008-07-01 
• Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.209 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Literature

Crystal Structure of the LpqC, Poly(3-hydroxybutyrate) Depolymerase from Bordetella parapertussis.

Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 68.72 kDa 
• Atom Count: 5,159 
• Modelled Residue Count: 580 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FMT	K [auth A], S [auth B], T [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	C [auth A], D [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.209 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.879	α = 90
b = 83.71	β = 92.68
c = 90.792	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXD	phasing
RESOLVE	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Kim, Y., Tesar, C., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary