6F9L | pdb_00006f9l

Crystal structure of Barley Beta-Amylase complexed with 3-Deoxy-3-fluoro-maltose

• PDB DOI: https://doi.org/10.2210/pdb6F9L/pdb

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


• Deposited: 2017-12-14 Released: 2019-01-30 
• Deposition Author(s): Tantanarat, K., Stevenson, C.E.M., Rejzek, M., Lawson, D.M., Field, R.A.
• Funding Organization(s): BBSRC Institute Strategic Programme on Understanding and Exploiting Metabolism (MET)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Barley Beta-Amylase complexed with 3-Deoxy-3-fluoro-maltose

Tantanarat, K., Stevenson, C.E.M., Rejzek, M., Lawson, D.M., Field, R.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.1 kDa 
• Atom Count: 4,293 
• Modeled 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-3-deoxy-3-fluoro-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G56701HV GlyCosmos:  G56701HV

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900073	B	3-Deoxy-3-fluoro-maltose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.08	α = 90
b = 99.41	β = 90
c = 64.76	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): Tantanarat, K., Stevenson, C.E.M., Rejzek, M., Lawson, D.M., 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

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• 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: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary