Download MendeleyThe Structure of a Bacteria Beta-Glucuronidase in Gh79 Family
Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.To be published.
5G0M | pdb_00005g0m
beta-glucuronidase with an activity-based probe (N-acyl cyclophellitol aziridine) bound
- PDB DOI: https://doi.org/10.2210/pdb5G0M/pdb
- Classification: HYDROLASE
- Organism(s): Acidobacterium capsulatum
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-03-21 Released: 2017-04-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213 (Depositor), 0.220 (DCC)
- R-Value Work: 0.183 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.184 (Depositor)
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| BETA-GLUCURONIDASE | 475 | Acidobacterium capsulatum | Mutation(s): 0 EC: 3.2.1.31 |  | |
UniProt | |||||
Find proteins for C1F2K5 (Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161)) Explore C1F2K5 Go to UniProtKB: C1F2K5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C1F2K5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| J13 Query on J13 | D [auth A] | (1S,2R,3R,4S,6S)-6-[(8-azidooctanoyl)amino]-2,3,4-trihydroxycyclohexane-1-carboxylate C15 H26 N4 O7 BTDXZNFDEBZDRR-KTEZLCCFSA-N |  | ||
| PO4 Query on PO4 | B [auth A], C [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213 (Depositor), 0.220 (DCC)
- R-Value Work: 0.183 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.184 (Depositor)
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 150.74 | α = 90 |
| b = 44.81 | β = 115.5 |
| c = 83.27 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2017-04-12 Deposition Author(s): Jin, Y., Wu, L., Jiang, J.B., Overkleeft, H.S., Davies, G.J.
Revision History (Full details and data files)
- Version 1.0: 2017-04-12
Type: Initial release - Version 1.1: 2019-05-22
Changes: Data collection, Derived calculations, Experimental preparation - Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description - Version 1.3: 2024-11-13
Changes: Structure summary
