3NNG | pdb_00003nng

Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis. Northeast Structural Genomics Consortium Target BfR258E

• PDB DOI: https://doi.org/10.2210/pdb3NNG/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-06-23 Released: 2010-08-18 
• Deposition Author(s): Vorobiev, S., Su, M., Dimaio, F., Baker, D., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Foote, E.L., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis.

Vorobiev, S., Su, M., Dimaio, F., Baker, D., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Foote, E.L., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.34 kDa 
• Atom Count: 2,529 
• Modeled Residue Count: 304 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	168	Bacteroides fragilis NCTC 9343	Mutation(s): 1  Gene Names: BF1314
UniProt
Find proteins for A0A380YW85 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore A0A380YW85  Go to UniProtKB:  A0A380YW85

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.208	α = 90
b = 62.463	β = 90
c = 72.001	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
Rosetta	phasing
CNS	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-18 
Deposition Author(s): Vorobiev, S., Su, M., Dimaio, F., Baker, D., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Foote, E.L., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-08-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-06
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description