3BYN
Crystal structure of B. subtilis levansucrase mutant E342A bound to raffinose
- PDB DOI: https://doi.org/10.2210/pdb3BYN/pdb
- Classification: TRANSFERASE
- Organism(s): Bacillus subtilis
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2008-01-16 Released: 2008-02-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.224 
- R-Value Work: 0.179 
- R-Value Observed: 0.181 
wwPDB Validation   3D Report Full Report
This is version 2.2 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 |
Levansucrase | 473 | Bacillus subtilis | Mutation(s): 1  Gene Names: SACB EC: 2.4.1.10 | ||
UniProt | |||||
Find proteins for P05655 (Bacillus subtilis (strain 168)) Explore P05655  Go to UniProtKB:  P05655 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05655 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900002 Query on PRD_900002 | B | raffinose | Oligosaccharide / Nutrient |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.224 
- R-Value Work: 0.179 
- R-Value Observed: 0.181 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 51.211 | α = 90 |
b = 66.7 | β = 90 |
c = 124.042 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2008-02-12  Deposition Author(s): Futterer, K., Meng, G.
Revision History (Full details and data files)
- Version 1.0: 2008-02-12
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2012-05-30
Changes: Non-polymer description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary - Version 2.1: 2021-11-10
Changes: Database references, Structure summary - Version 2.2: 2023-11-01
Changes: Data collection, Refinement description