6GSZ | pdb_00006gsz

Crystal structure of native alfa-L-rhamnosidase from Aspergillus terreus

PDB DOI: https://doi.org/10.2210/pdb6GSZ/pdb

Classification: HYDROLASE
Organism(s): Aspergillus terreus
Expression System: Aspergillus terreus
Mutation(s): No

Deposited: 2018-06-15 Released: 2018-11-14
Deposition Author(s): Pachl, P., Rezacova, P., Skerlova, J.
Funding Organization(s): Ministry of Education (Czech Republic)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.168 (Depositor), 0.169 (DCC)
R-Value Work:
0.134 (Depositor), 0.138 (DCC)
R-Value Observed:
0.136 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of native alpha-L-rhamnosidase from Aspergillus terreus.

Pachl, P., Skerlova, J., Simcikova, D., Kotik, M., Krenkova, A., Mader, P., Brynda, J., Kapesova, J., Kren, V., Otwinowski, Z., Rezacova, P.

(2018) Acta Crystallogr D Struct Biol 74: 1078-1084

PubMed: 30387766 Search on PubMed
DOI: https://doi.org/10.1107/S2059798318013049
Primary Citation Related Structures:
6GSZ

PubMed Abstract:
α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium. In addition to its catalytic domain, the α-L-rhamnosidase from A. terreus contains four accessory domains of unknown function. The structural data suggest that two of these accessory domains, E and F, might play a role in stabilizing the aglycon portion of the bound substrate.

Organizational Affiliation

Structural Biology, Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.

Macromolecule Content

Total Structure Weight: 105.55 kDa
Atom Count: 8,788
Modeled Residue Count: 863
Deposited Residue Count: 870
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-rhamnosidase	A	870	Aspergillus terreus	Mutation(s): 0 Gene Names: alpha-Rha EC: 3.2.1.40
UniProt
Find proteins for I0AZ41 (Aspergillus terreus) Explore I0AZ41 Go to UniProtKB: I0AZ41
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I0AZ41
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	7		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	5		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	6		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A]	DA [auth A], JA [auth A], KA [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Interactions & Density Focus chain DA [auth A] Focus chain JA [auth A] Focus chain KA [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
MPO Query on MPO Download:Ideal Coordinates CCD File SDF format, chain WA [auth A] MOL2 format, chain WA [auth A] mmCIF format, chain WA [auth A]	WA [auth A]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C₇ H₁₅ N O₄ S DVLFYONBTKHTER-UHFFFAOYSA-N		Interactions Focus chain WA [auth A] Interactions & Density Focus chain WA [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] MOL2 format, chain EA [auth A] mmCIF format, chain EA [auth A]	EA [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Interactions & Density Focus chain EA [auth A]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain XA [auth A] MOL2 format, chain XA [auth A] mmCIF format, chain XA [auth A]	XA [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain XA [auth A] Interactions & Density Focus chain XA [auth A]
DTU Query on DTU Download:Ideal Coordinates CCD File SDF format, chain PA [auth A] MOL2 format, chain PA [auth A] mmCIF format, chain PA [auth A]	PA [auth A]	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-ZXZARUISSA-N		Interactions Focus chain PA [auth A] Interactions & Density Focus chain PA [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain IA [auth A] SDF format, chain LA [auth A] SDF format, chain OA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain OA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain OA [auth A]	FA [auth A], IA [auth A], LA [auth A], OA [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain IA [auth A] Focus chain LA [auth A] Focus chain OA [auth A] Interactions & Density Focus chain FA [auth A] Focus chain IA [auth A] Focus chain LA [auth A] Focus chain OA [auth A]
PG0 Query on PG0 Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain MA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain MA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain MA [auth A]	GA [auth A], HA [auth A], MA [auth A]	2-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-UHFFFAOYSA-N		Interactions Focus chain GA [auth A] Focus chain HA [auth A] Focus chain MA [auth A] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain MA [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain NA [auth A] MOL2 format, chain NA [auth A] mmCIF format, chain NA [auth A]	NA [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain NA [auth A] Interactions & Density Focus chain NA [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A]	QA [auth A] RA [auth A] SA [auth A] TA [auth A] UA [auth A] QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Interactions & Density Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A]	AA [auth A] BA [auth A] CA [auth A] I [auth A] J [auth A] AA [auth A], BA [auth A], CA [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] 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] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] 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] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.168 (Depositor), 0.169 (DCC)
R-Value Work: 0.134 (Depositor), 0.138 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.26	α = 90
b = 106.248	β = 90
c = 119.832	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MLPHARE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Pachl, P.

Rezacova, P.

Skerlova, J.

Funding Organization	Location	Grant Number
Ministry of Education (Czech Republic)	Czech Republic	LO1304

Revision History (Full details and data files)

Version 1.0: 2018-11-14
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary