3P69

Crystal structure of a putative secreted protein (BF4250) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3P69/pdb

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


• Deposited: 2010-10-11 Released: 2010-10-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.219 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Crystal structure of a hypothetical protein (BF4250) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.76 kDa 
• Atom Count: 2,300 
• Modelled Residue Count: 256 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	134	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF4250
UniProt
Find proteins for Q5L7M9 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5L7M9  Go to UniProtKB:  Q5L7M9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 2.05 Å
• R-Value Free: 0.219 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: H 3 2
• Diffraction Data: https://doi.org/10.18430/M33P69

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.074	α = 90
b = 127.074	β = 90
c = 150.606	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
BUSTER-TNT	refinement
SCALA	data processing
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Structure summary
• Version 1.3: 2014-12-24
  Changes: Structure summary
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-02-01
  Changes: Database references, Derived calculations