3PU5 | pdb_00003pu5

The crystal structure of a putative extracellular solute-binding protein from Bordetella parapertussis

• PDB DOI: https://doi.org/10.2210/pdb3PU5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bordetella parapertussis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-03 Released: 2010-12-22 
• Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.220 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

The crystal structure of aa putative extracellular solute-binding protein from Bordetella parapertussis

Zhang, Z., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.13 kDa 
• Atom Count: 2,642 
• Modeled Residue Count: 322 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
extracellular solute-binding protein	A	333	Bordetella parapertussis	Mutation(s): 0  Gene Names: BPP0906
UniProt
Find proteins for Q7W0Z9 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7W0Z9  Go to UniProtKB:  Q7W0Z9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 2.05 Å
• R-Value Free:  0.220 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.569	α = 90
b = 104.862	β = 90
c = 39.3	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary