3GNR
Crystal Structure of a Rice Os3BGlu6 Beta-Glucosidase with covalently bound 2-deoxy-2-fluoroglucoside to the catalytic nucleophile E396
- PDB DOI: https://doi.org/10.2210/pdb3GNR/pdb
- Classification: HYDROLASE
- Organism(s): Oryza sativa Japonica Group
- Expression System: Escherichia coli
- Mutation(s): No 
- Membrane Protein: Yes  OPM
- Deposited: 2009-03-17 Released: 2009-07-21 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.81 Å
- R-Value Free: 0.185 
- R-Value Work: 0.162 
- R-Value Observed: 0.164 
This is version 1.3 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 |
Os03g0212800 protein | 488 | Oryza sativa Japonica Group | Mutation(s): 0  Gene Names: LOC_Os03g11420, Os03g0212800, Os3bglu6 locus ID: Os03g0212800 EC: 3.2.1.21 Membrane Entity: Yes  | ||
UniProt | |||||
Find proteins for Q8L7J2 (Oryza sativa subsp. japonica) Explore Q8L7J2  Go to UniProtKB:  Q8L7J2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q8L7J2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
G2F Query on G2F | B [auth A] | 2-deoxy-2-fluoro-alpha-D-glucopyranose C6 H11 F O5 ZCXUVYAZINUVJD-UKFBFLRUSA-N | |||
GOL Query on GOL | C [auth A], D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.81 Å
- R-Value Free: 0.185 
- R-Value Work: 0.162 
- R-Value Observed: 0.164 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 56.679 | α = 90 |
b = 90.591 | β = 90 |
c = 101.883 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-07-21  Deposition Author(s): Seshadri, S., Akiyama, T., Opassiri, R., Kuaprasert, B., Cairns, J.R.K.
Revision History (Full details and data files)
- Version 1.0: 2009-07-21
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations - Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary