5K6N
Structure of a GH3 b-glicosidase from cow rumen metagenome in complexed with xylose
- PDB DOI: https://doi.org/10.2210/pdb5K6N/pdb
- Classification: HYDROLASE
- Organism(s): metagenome
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-05-25 Released: 2016-10-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.08 Å
- R-Value Free: 0.213
- R-Value Work: 0.174
- R-Value Observed: 0.176
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 |
| B-GLUCOSIDASE | 921 | metagenome | Mutation(s): 0 Gene Names: glyA1 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| XYP Query on XYP | B [auth A] | beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N |  | ||
| SO4 Query on SO4 | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | I [auth A], J [auth A], K [auth A], L [auth A], M [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.08 Å
- R-Value Free: 0.213
- R-Value Work: 0.174
- R-Value Observed: 0.176
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.591 | α = 90 |
| b = 119.324 | β = 90 |
| c = 157.199 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2016-10-05 Deposition Author(s): Ramirez-Escudero, M., Sanz-Aparicio, J.
Revision History (Full details and data files)
- Version 1.0: 2016-10-05
Type: Initial release - Version 1.1: 2016-10-12
Changes: Database references - Version 1.2: 2016-11-23
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary
