1VB9
Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product
- PDB DOI: https://doi.org/10.2210/pdb1VB9/pdb
- Classification: HYDROLASE
- Organism(s): Thermoactinomyces vulgaris
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2004-02-25 Released: 2005-03-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.233 
- R-Value Work: 0.194 
- R-Value Observed: 0.194 
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 |
alpha-amylase II | 585 | Thermoactinomyces vulgaris | Mutation(s): 1  EC: 3.2.1.1 | ||
UniProt | |||||
Find proteins for Q08751 (Thermoactinomyces vulgaris) Explore Q08751  Go to UniProtKB:  Q08751 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q08751 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose | C, D | 6 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G33695HX GlyCosmos:  G33695HX GlyGen:  G33695HX |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | E [auth A], F [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.233 
- R-Value Work: 0.194 
- R-Value Observed: 0.194 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 113.049 | α = 90 |
b = 118.274 | β = 90 |
c = 112.107 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
MOSFLM | data reduction |
CCP4 | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2005-03-08  Deposition Author(s): Mizuno, M., Tonozuka, T., Uechi, A., Ohtaki, A., Ichikawa, K., Kamitori, S., Nishikawa, A., Sakano, Y.
Revision History (Full details and data files)
- Version 1.0: 2005-03-08
Type: Initial release - Version 1.1: 2008-04-27
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2021-11-10
Changes: Database references, Structure summary - Version 2.2: 2023-10-25
Changes: Data collection, Refinement description