6NWM

Structures of the transcriptional regulator BgaR, a lactose sensor.

• PDB DOI: https://doi.org/10.2210/pdb6NWM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Clostridium perfringens str. 13
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-06 Released: 2019-07-17 
• Deposition Author(s): Peat, T.S., Newman, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.233 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

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: 43.18 kDa 
• Atom Count: 2,869 
• Modelled Residue Count: 324 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator BgaR	A, B	182	Clostridium perfringens str. 13	Mutation(s): 0  Gene Names: CPE0770
UniProt
Find proteins for Q8XMB9 (Clostridium perfringens (strain 13 / Type A)) Explore Q8XMB9  Go to UniProtKB:  Q8XMB9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G57229GY GlyCosmos:  G57229GY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900038	C, D	lactulose	Oligosaccharide / Water retention

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.233 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.439	α = 90
b = 87.528	β = 90
c = 118.974	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Currently 6NWM does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2019-07-17 
Deposition Author(s): Peat, T.S., Newman, J.

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2019-07-24
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary