3SBU

Crystal structure of a ntf2-like protein (BF2862) from Bacteroides fragilis NCTC 9343 at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3SBU/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-06 Released: 2011-07-13 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.192 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Crystal structure of a Hypothetical ntf2-like protein (BF2862) from Bacteroides fragilis NCTC 9343 at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 63.54 kDa 
• Atom Count: 4,167 
• Modelled Residue Count: 460 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical ntf2-like protein	A, B	261	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF2862
UniProt
Find proteins for Q5LBG4 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5LBG4  Go to UniProtKB:  Q5LBG4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth A], K [auth A], L [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A, B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.192 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 6₁
• Diffraction Data: https://doi.org/10.18430/M33SBU

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.485	α = 90
b = 80.485	β = 90
c = 196.096	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations