Macromolecule Content

Total Structure Weight: 51169.23
Atom Count: 3478
Residue Count: 457
Unique protein chains: 1

3WH5

Crystal structure of GH1 beta-glucosidase Td2F2

DOI: 10.2210/pdb3WH5/pdb

Classification: HYDROLASE
Expression System: Escherichia coli

Deposited: 2013-08-21 Released: 2014-09-03
Deposition Author(s): Jo, T., Fushinobu, S., Uchiyama, T., Yaoi, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.6 Å
R-Value Free: 0.167
R-Value Work: 0.137

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity and transglycosylation activity of metagenomic beta-glucosidase Td2F2

Matsuzawa, T., Jo, T., Uchiyama, T., Manninen, J.A., Arakawa, T., Miyazaki, K., Fushinobu, S., Yaoi, K.

(2016) Febs J. --: --

PubMed: 27092463 Search on PubMed
DOI: 10.1111/febs.13743
Primary Citation of Related Structures:
5AYI, 5AYB, 3WH8, 3WH7, 3WH6

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
beta-glucosidase	A	457	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
NA Query on NA Download SDF File Download CCD File	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download SDF File Download CCD File	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
NHE Query on NHE Download SDF File Download CCD File	A	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID N-CYCLOHEXYLTAURINE; CHES C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.6 Å
R-Value Free: 0.167
R-Value Work: 0.137
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 68.802	α = 90.00
b = 69.624	β = 90.00
c = 96.057	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	refinement

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2013-08-21
Released Date: 2014-09-03
Deposition Author(s): Jo, T., Fushinobu, S., Uchiyama, T., Yaoi, K.

Revision History

Version 1.0: 2014-09-03
Type: Initial release
Version 1.1: 2016-05-04
Type: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.