5A7M | pdb_00005a7m

The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1)

PDB DOI: https://doi.org/10.2210/pdb5A7M/pdb

Classification: HYDROLASE
Organism(s): Trichoderma reesei
Expression System: Trichoderma reesei
Mutation(s): No

Deposited: 2015-07-08 Released: 2016-08-10
Deposition Author(s): Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Hansson, H., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.161 (Depositor), 0.161 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Th Crystal Structure of a Fungal Glycoside Hydrolase Family 3 Beta-Xylosidase, Xyl3A from Hypocrea Jecorina

Mikkelsen, N.E., Gudmundsson, M., Karkehabadi, S., Sandgren, M., Larenas, E., Mitchinson, C., Keleman, B., Kaper, T., Hansson, H.

To be published.

Macromolecule Content

Total Structure Weight: 178.26 kDa
Atom Count: 14,532
Modeled Residue Count: 1,527
Deposited Residue Count: 1,532
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-XYLOSIDASE	A, B	766	Trichoderma reesei	Mutation(s): 0 EC: 3.2.1.37
UniProt
Find proteins for Q92458 (Hypocrea jecorina) Explore Q92458 Go to UniProtKB: Q92458
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92458
Glycosylation
Glycosylation Sites: 9	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-(1-2)-alpha-D-mannopyranose-(1-3)-[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	C	7		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, J, K	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain J Focus chain K Interactions & Density Focus chain D Focus chain F Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-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	E, I	5		N-Glycosylation	Interactions Focus chain E Focus chain I Interactions & Density Focus chain E Focus chain I
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 5
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	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
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	H	4		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] 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] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] 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] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] 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]	EA [auth B] FA [auth B] GA [auth B] L [auth A] M [auth A] EA [auth B], FA [auth B], GA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] 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] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] 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]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain SA [auth B] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A], BA [auth A], SA [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain SA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain SA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain CA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain CA [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain CA [auth A]	CA [auth A], TA [auth B], UA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain TA [auth B] Focus chain UA [auth B] Interactions & Density Focus chain CA [auth A] Focus chain TA [auth B] Focus chain UA [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain RA [auth B] SDF format, chain R [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 NA [auth B] SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain R [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 NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain R [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 NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B]	HA [auth B] IA [auth B] JA [auth B] KA [auth B] LA [auth B] HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] 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 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 HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] 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 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]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain VA [auth B] SDF format, chain DA [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain DA [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain DA [auth A]	DA [auth A], VA [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth A] Focus chain VA [auth B] Interactions & Density Focus chain DA [auth A] Focus chain VA [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A, B	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.199 (Depositor), 0.199 (DCC)
R-Value Work: 0.161 (Depositor), 0.161 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.911	α = 90
b = 203.724	β = 90
c = 82.112	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
TRUNCATE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2018-01-17
Changes: Data collection
Version 2.0: 2020-03-11
Changes: Data collection, Derived calculations, Other, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2024-05-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.2: 2024-11-20
Changes: Structure summary