3GBV | pdb_00003gbv

Crystal structure of a putative LacI transcriptional regulator from Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb3GBV/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-20 Released: 2009-03-10 
• Deposition Author(s): Syed Ibrahim, B., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.240 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal structure of a putative LacI transcriptional regulator from Bacteroides fragilis

Syed Ibrahim, B., Kumaran, D., Burley, S.K., Swaminathan, S.

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: 71.35 kDa 
• Atom Count: 4,916 
• Modeled Residue Count: 576 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative LacI-family transcriptional regulator	A, B	304	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF2720
UniProt
Find proteins for A0A381D6S6 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore A0A381D6S6  Go to UniProtKB:  A0A381D6S6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.240 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.976	α = 90
b = 240.568	β = 90
c = 119.214	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Syed Ibrahim, B., Kumaran, D., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary