3DKZ

Crystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis. Northeast Structural Genomics Consortium target BpR208C.

• PDB DOI: https://doi.org/10.2210/pdb3DKZ/pdb

• Classification: HYDROLASE
• Organism(s): Bordetella parapertussis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-26 Released: 2008-08-26 
• Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., 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: 2.40 Å
• R-Value Free: 
  0.260 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Crystal structure of the Q7W9W5_BORPA protein from Bordetella parapertussis.

Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.16 kDa 
• Atom Count: 1,894 
• Modelled Residue Count: 249 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase superfamily protein	A, B	142	Bordetella parapertussis	Mutation(s): 0  Gene Names: BPP1634
UniProt
Find proteins for Q7W9W5 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7W9W5  Go to UniProtKB:  Q7W9W5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.646	α = 90
b = 69.646	β = 90
c = 107.792	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXDE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Vorobiev, S.M., Su, M., Seetharaman, J., Wang, D., Ciccosanti, C., Foote, E.L., Mao, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary