5TF0 | pdb_00005tf0

Crystal Structure of Glycosil Hydrolase Family 3 N-Terminal Domain Protein from Bacteroides intestinalis

• PDB DOI: https://doi.org/10.2210/pdb5TF0/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides intestinalis DSM 17393
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-23 Released: 2016-10-05 
• Deposition Author(s): Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal Structure of Glycosil Hydrolase Family 3 N-Terminal Domain Protein from Bacteroides intestinalis

Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A., MCSG

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: 168.27 kDa 
• Atom Count: 11,824 
• Modeled Residue Count: 1,466 
• Deposited Residue Count: 1,502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 3 N-terminal domain protein	A, B	751	Bacteroides intestinalis DSM 17393	Mutation(s): 0  Gene Names: BACINT_00768 EC: 3.2.1.21
UniProt
Find proteins for B3C777 (Bacteroides intestinalis DSM 17393) Explore B3C777  Go to UniProtKB:  B3C777

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], 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: 2.20 Å
• R-Value Free:  0.264 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.57	α = 90
b = 88.447	β = 97.89
c = 107.282	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Kim, Y., Hatzos-Skintges, C., Endres, M., Babnigg, G., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Source and taxonomy
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary