4GPN
The crystal structure of 6-P-beta-D-Glucosidase (E375Q mutant) from Streptococcus mutans UA150 in complex with Gentiobiose 6-phosphate.
- PDB DOI: https://doi.org/10.2210/pdb4GPN/pdb
- Classification: HYDROLASE
- Organism(s): Streptococcus mutans UA159
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2012-08-21 Released: 2012-10-03 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.239 
- R-Value Work: 0.177 
- R-Value Observed: 0.180 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
6-phospho-beta-D-Glucosidase | 480 | Streptococcus mutans UA159 | Mutation(s): 1  Gene Names: bgl, SMU_1601 EC: 3.2.1.86 | ||
UniProt | |||||
Find proteins for Q8DT00 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DT00  Go to UniProtKB:  Q8DT00 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8DT00 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
TRS Query on TRS | E [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
GOL Query on GOL | F [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900069 Query on PRD_900069 | C, D | gentiobiose 6-phosphate | Oligosaccharide / Substrate analog |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.239 
- R-Value Work: 0.177 
- R-Value Observed: 0.180 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 58.22 | α = 90 |
b = 91.796 | β = 102.23 |
c = 94.225 | γ = 90 |
Software Name | Purpose |
---|---|
SBC-Collect | data collection |
MOLREP | phasing |
PHENIX | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2012-10-03  Deposition Author(s): Tan, K., Michalska, K., Li, H., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2012-10-03
Type: Initial release - Version 1.1: 2017-11-15
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary