6F9H | pdb_00006f9h

Crystal structure of Barley Beta-Amylase complexed with 4-S-alpha-D-glucopyranosyl-(1,4-dideoxy-4-thio-nojirimycin)

• PDB DOI: https://doi.org/10.2210/pdb6F9H/pdb

• Classification: HYDROLASE
• Organism(s): Hordeum vulgare
• Mutation(s): Yes 


• Deposited: 2017-12-14 Released: 2019-01-30 
• Deposition Author(s): Moncayo, M.A., Rodrigues, L.L., Stevenson, C.E.M., Ruzanski, C., Rejzek, M., Lawson, D.M., Angulo, J., Field, R.A.
• Funding Organization(s): BBSRC Institute Strategic Programme on Understanding and Exploiting Metabolism (MET), John Innes Foundation, Royal Society Newton Fund Fellowship

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Synthesis, biological and structural analysis of prospective glycosyl-iminosugar prodrugs: impact on germination

Moncayo, M.A., Rodrigues, L.L., Stevenson, C.E.M., Ruzanski, C., Rejzek, M., Lawson, D.M., Angulo, J., Field, R.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.11 kDa 
• Atom Count: 4,315 
• Modelled Residue Count: 485 
• Deposited Residue Count: 535 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-amylase	A	535	Hordeum vulgare	Mutation(s): 1  EC: 3.2.1.2
UniProt
Find proteins for A8CFR3 (Hordeum vulgare) Explore A8CFR3  Go to UniProtKB:  A8CFR3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	C [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
SGJ	B [auth A]	1,4-dideoxy-4-thio-nojirimycin C6 H13 N O3 S NSHHSUUKQHDEOL-JGWLITMVSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.52	α = 90
b = 99.11	β = 90
c = 65.04	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Moncayo, M.A., Rodrigues, L.L., Stevenson, C.E.M., Ruzanski, C., Rejzek, M., Lawson, D.M., Angulo, J., Field, R.A.

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Funding Organization	Location	Grant Number
BBSRC Institute Strategic Programme on Understanding and Exploiting Metabolism (MET)	United Kingdom	BB/J004561/1
John Innes Foundation	United Kingdom	--
Royal Society Newton Fund Fellowship	United Kingdom	--

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary