3EJN

CRYSTAL STRUCTURE OF A SUSD HOMOLOG (BF3025) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.50 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3EJN/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-18 Released: 2008-09-30 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.168 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Crystal structure of SusD homolog (YP_212639.1) from Bacteroides fragilis NCTC 9343 at 1.50 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.72 kDa 
• Atom Count: 4,246 
• Modelled Residue Count: 450 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD homolog	A	474	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: YP_212639.1, BF3025
UniProt
Find proteins for A0A380YV80 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore A0A380YV80  Go to UniProtKB:  A0A380YV80

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A], C [auth A], D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
FMT	E [auth A], F [auth A], G [auth A], H [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.168 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: H 3
• Diffraction Data: https://doi.org/10.18430/M33EJN

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.99	α = 90
b = 166.99	β = 90
c = 48.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations