4JX0 | pdb_00004jx0

Crystal structure of a two domain protein with unknown function (BF3416) from Bacteroides fragilis NCTC 9343 at 2.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4JX0/pdb

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


• Deposited: 2013-03-27 Released: 2013-05-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of a hypothetical protein (BF3416) from Bacteroides fragilis NCTC 9343 at 2.90 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 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.94 kDa 
• Atom Count: 4,961 
• Modeled Residue Count: 604 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B	320	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF3416, BF9343_3326, YP_213022.1
UniProt
Find proteins for Q5L9W9 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5L9W9  Go to UniProtKB:  Q5L9W9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	C [auth A], D [auth A], F [auth B], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.90 Å
• R-Value Free:  0.229 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34JX0

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.341	α = 90
b = 118.742	β = 90
c = 239.871	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-09
  Changes: Data collection, Structure summary