3BS3 | pdb_00003bs3

Crystal structure of a putative DNA-binding protein from Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb3BS3/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-12-21 Released: 2008-01-15 
• Deposition Author(s): Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.219 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

The structure of a putative DNA-binding protein from Bacteroides fragilis.

Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 9.15 kDa 
• Atom Count: 667 
• Modeled Residue Count: 62 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative DNA-binding protein	A	76	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF1076
UniProt
Find proteins for Q5LGD2 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LGD2  Go to UniProtKB:  Q5LGD2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.219 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.337	α = 90
b = 63.337	β = 90
c = 34.706	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-15 
Deposition Author(s): Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary