5O47 | pdb_00005o47

Structure of D80A-fructofuranosidase from Xanthophyllomyces dendrorhous complexed with fructosyl-hydroxytyrosol

PDB DOI: https://doi.org/10.2210/pdb5O47/pdb

Classification: HYDROLASE
Organism(s): Phaffia rhodozyma
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2017-05-26 Released: 2018-11-28
Deposition Author(s): Ramirez-Escudero, M., Sanz-Aparicio, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.182 (Depositor), 0.191 (DCC)
R-Value Work:
0.168 (Depositor), 0.177 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Fructosylation of Hydroxytyrosol by the beta-Fructofuranosidase from Xanthophyllomyces dendrorhous: Insights into the Molecular Basis of the Enzyme Specificity

Ramirez-Escudero, M., Poveda, a., Ballesteros, A.O., Plou, F.J.

(2018) ChemCatChem

DOI: https://doi.org/10.1002/cctc.201801171

Macromolecule Content

Total Structure Weight: 159.36 kDa
Atom Count: 12,016
Modeled Residue Count: 1,248
Deposited Residue Count: 1,330
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-fructofuranosidase	A, B	665	Phaffia rhodozyma	Mutation(s): 1 Gene Names: INV
UniProt
Find proteins for J7HDY4 (Phaffia rhodozyma) Explore J7HDY4 Go to UniProtKB: J7HDY4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J7HDY4
Glycosylation
Glycosylation Sites: 15	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
alpha-D-mannopyranose-(1-3)-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, F	6		N-Glycosylation	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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, G	10		N-Glycosylation	Interactions Focus chain D Focus chain G Interactions & Density Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

Entity ID: 4
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, H	2		N-Glycosylation	Interactions Focus chain E Focus chain H Interactions & Density Focus chain E Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9OK Query on 9OK Download:Ideal Coordinates CCD File SDF format, chain XA [auth B] SDF format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain X [auth A]	X [auth A], XA [auth B]	2-(3,4-dihydroxyphenyl)ethyl beta-D-fructofuranoside C₁₄ H₂₀ O₈ LKYHMBCDFKCNAO-YIYPIFLZSA-N		Interactions Focus chain X [auth A] Focus chain XA [auth B] Interactions & Density Focus chain X [auth A] Focus chain XA [auth B]
9WZ Query on 9WZ Download:Ideal Coordinates CCD File SDF format, chain YA [auth B] SDF format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Y [auth A]	Y [auth A], YA [auth B]	2-hydroxy-4-(2-hydroxyethyl)phenyl beta-D-fructofuranoside C₁₄ H₂₀ O₈ CNXXGYXVIZNKJW-YIYPIFLZSA-N		Interactions Focus chain Y [auth A] Focus chain YA [auth B] Interactions & Density Focus chain Y [auth A] Focus chain YA [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain VA [auth B] SDF format, chain SA [auth B] SDF format, chain S [auth A] SDF format, chain QA [auth B] SDF format, chain Q [auth A] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain J [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] LA [auth B] I [auth A], J [auth A], K [auth A], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B]
975 Query on 975 Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	Z [auth A], ZA [auth B]	4-(2-hydroxyethyl)benzene-1,2-diol C₈ H₁₀ O₃ JUUBCHWRXWPFFH-UHFFFAOYSA-N		Interactions Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain Z [auth A] Focus chain ZA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GB [auth B] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain KB [auth B] SDF format, chain JB [auth B] SDF format, chain IB [auth B] SDF format, chain IA [auth A] SDF format, chain HB [auth B] SDF format, chain HA [auth A] SDF format, chain GA [auth A] SDF format, chain EB [auth B] SDF format, chain EA [auth A] SDF format, chain DB [auth B] SDF format, chain DA [auth A] SDF format, chain CB [auth B] SDF format, chain BB [auth B] SDF format, chain BA [auth A] SDF format, chain AB [auth B] SDF format, chain AA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain JB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain JB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AA [auth A]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CA [auth A] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CA [auth A], CB [auth B], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HA [auth A], HB [auth B], IA [auth A], IB [auth B], JA [auth A], JB [auth B], KA [auth A], KB [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.182 (Depositor), 0.191 (DCC)
R-Value Work: 0.168 (Depositor), 0.177 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.616	α = 90
b = 205.356	β = 90
c = 146.94	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-11-28

Deposition Author(s):

Ramirez-Escudero, M.

Sanz-Aparicio, J.

Revision History (Full details and data files)

Version 1.0: 2018-11-28
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: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary