3CEW

Crystal structure of a cupin protein (BF4112) from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR205

• PDB DOI: https://doi.org/10.2210/pdb3CEW/pdb

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


• Deposited: 2008-02-29 Released: 2008-03-25 
• Deposition Author(s): Forouhar, F., Chen, Y., Seetharaman, J., Mao, L., Xiao, R., Ciccosanti, C., Foote, E.L., Maglaqui, M., Wang, H., Baran, M.C., Acton, T.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: 2.31 Å
• R-Value Free: 0.246 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Crystal structure of a cupin protein (BF4112) from Bacteroides fragilis. Northeast Structural Genomics Consortium target BfR205.

Forouhar, F., Chen, Y., Seetharaman, J., Mao, L., Xiao, R., Ciccosanti, C., Foote, E.L., Maglaqui, M., Wang, H., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 55.32 kDa 
• Atom Count: 3,869 
• Modelled Residue Count: 472 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized cupin protein	A, B, C, D	125	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF4112
UniProt
Find proteins for A0A380YRY7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore A0A380YRY7  Go to UniProtKB:  A0A380YRY7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.246 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.14	α = 90
b = 87.834	β = 90
c = 128.032	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Forouhar, F., Chen, Y., Seetharaman, J., Mao, L., Xiao, R., Ciccosanti, C., Foote, E.L., Maglaqui, M., Wang, H., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary