3I4G

CRYSTAL STRUCTURE OF A SUSD-LIKE CARBOHYDRATE BINDING PROTEIN (BF0978) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.35 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3I4G/pdb

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


• Deposited: 2009-07-01 Released: 2009-07-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.157 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 

Literature

Crystal structure of SusD-like carbohydrate binding protein BF1063 from Bacteroides fragilis YCH46 (YP_210668.1) from Bacteroides fragilis NCTC 9343 at 1.35 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.64 kDa 
• Atom Count: 5,133 
• Modelled Residue Count: 513 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SusD-like carbohydrate binding protein BF1063	A	528	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF0978, YP_210668.1
UniProt
Find proteins for Q5LGM0 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5LGM0  Go to UniProtKB:  Q5LGM0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.35 Å
• R-Value Free: 0.157 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M33I4G

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.685	α = 90
b = 66.415	β = 90
c = 162.74	γ = 90

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: 2009-07-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, 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