4YIC

CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID

• PDB DOI: https://doi.org/10.2210/pdb4YIC/pdb

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


• Deposited: 2015-03-01 Released: 2015-04-01 
• 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: 1.60 Å
• R-Value Free: 0.173 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF A TRAP TRANSPORTER SOLUTE BINDING PROTEIN (IPR025997) FROM BORDETELLA BRONCHISEPTICA RB50 (BB0280, TARGET EFI-500035) WITH BOUND PICOLINIC ACID

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: 85.65 kDa 
• Atom Count: 6,147 
• Modelled Residue Count: 687 
• Deposited Residue Count: 770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRAP TRANSPORTER SOLUTE BINDING PROTEIN	A, B	385	Bordetella bronchiseptica RB50	Mutation(s): 0
UniProt
Find proteins for A0A0J9X284 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0J9X284  Go to UniProtKB:  A0A0J9X284

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6PC	F [auth A], J [auth B]	PYRIDINE-2-CARBOXYLIC ACID C6 H5 N O2 SIOXPEMLGUPBBT-UHFFFAOYSA-N
IMD	G [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ACT	D [auth A], E [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.173 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.681	α = 90
b = 86.141	β = 100.86
c = 72.339	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-04-01 
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: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• 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