3F9U

Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from Bacteroides fragilis

• PDB DOI: https://doi.org/10.2210/pdb3F9U/pdb

• Classification: structural genomics, unknown function
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-14 Released: 2008-12-02 
• Deposition Author(s): Chang, C., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Crystal structure of C-terminal domain of putative exported cytochrome C biogenesis-related protein from Bacteroides fragilis

Chang, C., Tesar, C., Cobb, G., Joachimiak, A.

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)

Macromolecule Content

• Total Structure Weight: 40.4 kDa 
• Atom Count: 2,657 
• Modelled Residue Count: 293 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative exported cytochrome C biogenesis-related protein	A, B	172	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF3033 EC: 1.8.1.8
UniProt
Find proteins for Q5LAZ4 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LAZ4  Go to UniProtKB:  Q5LAZ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	C [auth A], D [auth A], F [auth A], H [auth A], I [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

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: 2.20 Å
• R-Value Free: 0.236 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.16	α = 90
b = 64.16	β = 90
c = 181.555	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-02 
Deposition Author(s): Chang, C., Tesar, C., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-12-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-10-09
  Changes: Structure summary