6B6L | pdb_00006b6l

The crystal structure of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus DSM 14838

• PDB DOI: https://doi.org/10.2210/pdb6B6L/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides cellulosilyticus DSM 14838
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-10-02 Released: 2017-10-11 
• Deposition Author(s): Tan, K., Joachimiak, G., Nocek, B., Enddres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

The crystal structure of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus DSM 14838

Tan, K., Joachimiak, G., Nocek, B., Enddres, M., Babnigg, G., Joachimiak, A.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 175.71 kDa 
• Atom Count: 12,209 
• Modeled Residue Count: 1,453 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyl hydrolase family 2, sugar binding domain protein	A, B	776	Bacteroides cellulosilyticus DSM 14838	Mutation(s): 0  Gene Names: BACCELL_00063
UniProt
Find proteins for E2N721 (Bacteroides cellulosilyticus DSM 14838) Explore E2N721  Go to UniProtKB:  E2N721

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	E [auth A], F [auth A], H [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
CSD	A, B	CYS	Oxidation	C3 H7 N O4 S
CSD	A, B	CYS	Hydroxylation	C3 H7 N O4 S
MSE	A, B	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.528	α = 90
b = 227.135	β = 108.83
c = 66.902	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Tan, K., Joachimiak, G., Nocek, B., Enddres, M., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2017-10-18
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary