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)

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8CFR3
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900073 Query on PRD_900073	B	3-Deoxy-3-fluoro-maltose	Oligosaccharide / Substrate analog		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.199 (Depositor)
R-Value Work: 0.159 (Depositor)
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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Funding Organization	Location	Grant Number
BBSRC Institute Strategic Programme on Understanding and Exploiting Metabolism (MET)	United Kingdom	BB/J004561/1

Revision History (Full details and data files)

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