5FRE
Characterization of a novel CBM from Clostridium perfringens
- PDB DOI: https://doi.org/10.2210/pdb5FRE/pdb
- Classification: HYDROLASE
- Organism(s): Clostridium perfringens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2015-12-17 Released: 2016-07-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.209 
- R-Value Work: 0.173 
- R-Value Observed: 0.175 
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 |
EXO-ALPHA-SIALIDASE | 194 | Clostridium perfringens | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for A0A0H2YQR1 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)) Explore A0A0H2YQR1  Go to UniProtKB:  A0A0H2YQR1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A0A0H2YQR1 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
1PG Query on 1PG | J [auth A], N [auth B] | 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N | |||
ACT Query on ACT | O [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M | |||
CA Query on CA | G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.209 
- R-Value Work: 0.173 
- R-Value Observed: 0.175 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 64.348 | α = 90 |
b = 76.714 | β = 93.46 |
c = 67.254 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2016-07-20  Deposition Author(s): Ribeiro, J., Pau, W., Pifferi, C., Renaudet, O., Varrot, A., Mahal, L.K., Imberty, A.
Revision History (Full details and data files)
- Version 1.0: 2016-07-20
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary