4BQ5
Structural analysis of an exo-beta-agarase
- PDB DOI: https://doi.org/10.2210/pdb4BQ5/pdb
- Classification: HYDROLASE
- Organism(s): Saccharophagus degradans 2-40
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2013-05-29 Released: 2013-08-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.251 
- R-Value Work: 0.189 
- R-Value Observed: 0.192 
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 |
B-AGARASE | 750 | Saccharophagus degradans 2-40 | Mutation(s): 1  EC: 3.2.1.81 | ||
UniProt | |||||
Find proteins for Q21HC5 (Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024)) Explore Q21HC5  Go to UniProtKB:  Q21HC5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q21HC5 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GAL Query on GAL | J [auth A] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N | |||
AAL Query on AAL | I [auth A] | 3,6-anhydro-alpha-L-galactopyranose C6 H10 O5 DCQFFOLNJVGHLW-DSOBHZJASA-N | |||
GOL Query on GOL | K [auth A], O [auth B], P [auth B], Q [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CA Query on CA | L [auth A] M [auth A] N [auth A] R [auth B] S [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.251 
- R-Value Work: 0.189 
- R-Value Observed: 0.192 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 69.03 | α = 90 |
b = 116.17 | β = 90 |
c = 207.97 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2013-08-14  Deposition Author(s): Pluvinage, B., Hehemann, J.H., Boraston, A.B.
Revision History (Full details and data files)
- Version 1.0: 2013-08-14
Type: Initial release - Version 1.1: 2013-08-21
Changes: Database references - Version 1.2: 2013-08-28
Changes: Atomic model, Data collection, Derived calculations - Version 1.3: 2013-10-16
Changes: Database references - Version 1.4: 2020-07-01
Changes: Advisory, Data collection, Derived calculations, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-12-20
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary