4YZZ

Crystal structure of a TRAP transporter solute binding protein (IPR025997) from Bordetella bronchiseptica RB50 (BB0280, TARGET EFI-500035) mixed occupancy dimer, copurified calcium and picolinate bound active site versus apo site

• PDB DOI: https://doi.org/10.2210/pdb4YZZ/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bordetella bronchiseptica RB50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-25 Released: 2015-05-20 
• Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)
• 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: 1.30 Å
• R-Value Free: 0.163 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

Starting Model: experimental

Literature

Crystal structure of a TRAP transporter solute binding protein (IPR025997) from Bordetella bronchiseptica RB50 (BB0280, TARGET EFI-500035) mixed occupancy dimer, copurified calcium and picolinate bound active site versus apo site

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 81.06 kDa 
• Atom Count: 6,260 
• Modelled Residue Count: 672 
• Deposited Residue Count: 734 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP TRANSPORTER SOLUTE BINDING PROTEIN	A, B [auth D]	367	Bordetella bronchiseptica RB50	Mutation(s): 0
UniProt
Find proteins for A0A0H3LP08 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LP08  Go to UniProtKB:  A0A0H3LP08

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	G [auth D]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
6PC	F [auth A]	PYRIDINE-2-CARBOXYLIC ACID C6 H5 N O2 SIOXPEMLGUPBBT-UHFFFAOYSA-N
PEG	D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.163 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.249	α = 90
b = 50.104	β = 104.47
c = 96.556	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM093342

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description