4FRY

The structure of a putative signal-transduction protein with CBS domains from Burkholderia ambifaria MC40-6

• PDB DOI: https://doi.org/10.2210/pdb4FRY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Burkholderia ambifaria MC40-6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-26 Released: 2012-07-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.267 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L., Gallagher, L.A., Patrapuvich, R., Clifton, M.C., Gardberg, A.S., Edwards, T.E., Armour, B., Begley, D.W., Dieterich, S.H., Dranow, D.M., Abendroth, J., Fairman, J.W., Fox, D., Staker, B.L., Phan, I., Gillespie, A., Choi, R., Nakazawa-Hewitt, S., Nguyen, M.T., Napuli, A., Barrett, L., Buchko, G.W., Stacy, R., Myler, P.J., Stewart, L.J., Manoil, C., Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851

• PubMed: 23382856 
• DOI: https://doi.org/10.1371/journal.pone.0053851
• Primary Citation of Related Structures:  
  3D63, 3DAH, 3EIZ, 3EJ2, 3EK2, 3EZO, 3F0F, 3FTP, 3GK0, 3GK3, 3GVF, 3GWA, 3GWE, 3IML, 3SZ8, 3T4C, 3TML, 3TMQ, 3TXY, 3U7J, 3UE9, 3UK1, 3UK2, 3UND, 3URR, 3UW1, 3UW2, 3UW3, 3V2I, 3V7N, 3V8H, 3V9O, 3V9P, 3VAV, 4DDO, 4DFE, 4DHE, 4DHK, 4DUT, 4DZ4, 4E4T, 4EFI, 4EG0, 4EGJ, 4EK2, 4EQY, 4EWG, 4EXQ, 4F2G, 4F32


• PubMed Abstract: 
  

  The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite.

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Organizational Affiliation: 

Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.

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: 36.34 kDa 
• Atom Count: 2,136 
• Modelled Residue Count: 274 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative signal-transduction protein with CBS domains	A, B	157	Burkholderia ambifaria MC40-6	Mutation(s): 0  Gene Names: BamMC406_4587
UniProt
Find proteins for B1YXI0 (Burkholderia ambifaria (strain MC40-6)) Explore B1YXI0  Go to UniProtKB:  B1YXI0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
AMP	D [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.267 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.35	α = 90
b = 56.63	β = 98.41
c = 76.58	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2013-10-30
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description