3ONQ | pdb_00003onq

Crystal Structure of Regulator of Polyketide Synthase Expression BAD_0249 from Bifidobacterium adolescentis

• PDB DOI: https://doi.org/10.2210/pdb3ONQ/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Bifidobacterium adolescentis ATCC 15703
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-08-30 Released: 2010-09-08 
• Deposition Author(s): Kim, Y., Wu, R., Tan, K., Morales, J., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Crystal Structure of Regulator of Polyketide Synthase Expression BAD_0249 from Bifidobacterium adolescentis

Kim, Y., Wu, R., Tan, K., Morales, J., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119 kDa 
• Atom Count: 8,645 
• Modeled Residue Count: 994 
• Deposited Residue Count: 1,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of polyketide synthase expression	A, B, C, D	262	Bifidobacterium adolescentis ATCC 15703	Mutation(s): 0  Gene Names: BAD_0249
UniProt
Find proteins for A0ZZZ7 (Bifidobacterium adolescentis (strain ATCC 15703 / DSM 20083 / NCTC 11814 / E194a)) Explore A0ZZZ7  Go to UniProtKB:  A0ZZZ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth C], BA [auth C], E [auth A], F [auth A], G [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], N [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], H [auth A], M [auth A], MA [auth D], T [auth B], U [auth B], V [auth B], W [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.452	α = 90
b = 93.452	β = 90
c = 166.687	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXS	phasing
MLPHARE	phasing
BUCCANEER	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Kim, Y., Wu, R., Tan, K., Morales, J., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary