5IX8 | pdb_00005ix8

Crystal structure of sugar ABC transport system, substrate-binding protein from Bordetella parapertussis 12822

• PDB DOI: https://doi.org/10.2210/pdb5IX8/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bordetella parapertussis 12822
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-03-23 Released: 2016-04-06 
• Deposition Author(s): Chang, C., Cuff, M., Joachimiak, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Literature

Crystal structure of sugar ABC transport system, substrate-binding protein from Bordetella parapertussis 12822

Chang, C., Cuff, M., Joachimiak, G., Clancy, S., 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: 70.87 kDa 
• Atom Count: 5,558 
• Modeled Residue Count: 639 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar ABC transport system, substrate-binding protein	A, B	321	Bordetella parapertussis 12822	Mutation(s): 0  Gene Names: BPP2773
UniProt
Find proteins for Q7W6X1 (Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)) Explore Q7W6X1  Go to UniProtKB:  Q7W6X1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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: 1.60 Å
• R-Value Free:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.557	α = 90
b = 78.719	β = 104.83
c = 66.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-06 
Deposition Author(s): Chang, C., Cuff, M., Joachimiak, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM 115586

Revision History  

• Version 1.0: 2016-04-06
  Type: Initial release
  
• Version 1.1: 2016-08-17
  Changes: Structure summary
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary