6Q3R | pdb_00006q3r

ASPERGILLUS ACULEATUS GALACTANASE

PDB DOI: https://doi.org/10.2210/pdb6Q3R/pdb

Classification: HYDROLASE
Organism(s): Aspergillus aculeatus
Mutation(s): No

Deposited: 2018-12-04 Released: 2019-06-12
Deposition Author(s): Muderspach, S.J., Torpenholt, S., Lo Leggio, L., Poulsen, J.C.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.211 (Depositor), 0.214 (DCC)
R-Value Work:
0.145 (Depositor), 0.154 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structure of Aspergillus aculeatus beta-1,4-galactanase in complex with galactobiose.

Torpenholt, S., Poulsen, J.C.N., Muderspach, S.J., De Maria, L., Lo Leggio, L.

(2019) Acta Crystallogr F Struct Biol Commun 75: 399-404

PubMed: 31204685 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X19005612
Primary Citation Related Structures:
6Q3R

PubMed Abstract:
β-1,4-Galactanases are glycoside hydrolases that are involved in the degradation of pectin and belong to family 53 in the classification of glycoside hydrolases. Previous studies have elucidated the structures of several fungal and two bacterial galactanases, while biochemical studies have indicated differences in the product profiles of different members of the family. Structural studies of ligand complexes have to date been limited to the bacterial members of the family. Here, the first structure of a fungal galactanase in complex with a disaccharide is presented. Galactobiose binds to subsites -1 and -2, thus improving our understanding of ligand binding to galactanases.

Organizational Affiliation

Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.

Macromolecule Content

Total Structure Weight: 77.9 kDa
Atom Count: 5,711
Modeled Residue Count: 668
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arabinogalactan endo-beta-1,4-galactanase	A, B	334	Aspergillus aculeatus	Mutation(s): 0 EC: 3.2.1.89
UniProt
Find proteins for P48842 (Aspergillus aculeatus) Explore P48842 Go to UniProtKB: P48842
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48842
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, F	3		N-Glycosylation	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-beta-D-galactopyranose	D, E	2		N/A	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G08806VI GlyCosmos: G08806VI GlyGen: G08806VI

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A] mmCIF format, chain W [auth A]	W [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain CA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain CA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain CA [auth B]	CA [auth B], M [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain M [auth A] Interactions & Density Focus chain CA [auth B] Focus chain M [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] MOL2 format, chain KA [auth B] mmCIF format, chain KA [auth B]	KA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Interactions & Density Focus chain KA [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth A], X [auth B], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain X [auth B] Focus chain Y [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain IA [auth B] SDF format, chain O [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain DA [auth B]	DA [auth B] EA [auth B] FA [auth B] GA [auth B] HA [auth B] DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain V [auth A] SDF format, chain U [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A]	JA [auth B], U [auth A], V [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain JA [auth B] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain JA [auth B] Focus chain U [auth A] Focus chain V [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain Z [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain BA [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth B]	AA [auth B] BA [auth B] I [auth A] J [auth A] K [auth A] AA [auth B], BA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Z [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900113 Query on PRD_900113	D, E	4beta-beta-galactobiose	Oligosaccharide / Metabolism		Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.211 (Depositor), 0.214 (DCC)
R-Value Work: 0.145 (Depositor), 0.154 (DCC)
R-Value Observed: 0.148 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.2	α = 90
b = 200.2	β = 90
c = 106.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-06-12
Type: Initial release
Version 1.1: 2019-06-26
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary