3PTM
The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with 2-fluoroglucopyranoside
- PDB DOI: https://doi.org/10.2210/pdb3PTM/pdb
- Classification: HYDROLASE
- Organism(s): Oryza sativa
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-12-03 Released: 2011-05-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.234
- R-Value Work: 0.196
- R-Value Observed: 0.198
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 |
| Beta-glucosidase Os4BGlu12 | 505 | Oryza sativa | Mutation(s): 0 Gene Names: Os04g0474800 EC: 3.2.1.21 |  | |
UniProt | |||||
Find proteins for B8AVF0 (Oryza sativa subsp. indica) Explore B8AVF0 Go to UniProtKB: B8AVF0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B8AVF0 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| G2F Query on G2F | C [auth A], I [auth B] | 2-deoxy-2-fluoro-alpha-D-glucopyranose C6 H11 F O5 ZCXUVYAZINUVJD-UKFBFLRUSA-N |  | ||
| GOL Query on GOL | E [auth A] F [auth A] G [auth A] H [auth A] J [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | D [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.234
- R-Value Work: 0.196
- R-Value Observed: 0.198
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.046 | α = 90 |
| b = 114.046 | β = 90 |
| c = 184.149 | γ = 90 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2011-05-18 Deposition Author(s): Sansenya, S., Opassiri, R., Kuaprasert, B., Chen, C.J., Ketudat Cairns, J.R.
Revision History (Full details and data files)
- Version 1.0: 2011-05-18
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations - Version 1.3: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary
