4XX6 | pdb_00004xx6

Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Gloeophyllum trabeum

PDB DOI: https://doi.org/10.2210/pdb4XX6/pdb

Classification: HYDROLASE
Organism(s): Gloeophyllum trabeum ATCC 11539
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2015-01-29 Released: 2015-02-11
Deposition Author(s): Stogios, P.J., Nocek, B., Xu, X., Cui, H., Lowden, M., Savchenko, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.204 (Depositor), 0.200 (DCC)
R-Value Work:
0.154 (Depositor), 0.150 (DCC)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of a glycosylated endo-beta-1,4-xylanase (glycoside hydrolase family 10/GH10) enzyme from Gloeophyllum trabeum.

Stogios, P.J., Xu, X., Cui, H., Lowden, M., Savchenko, A.

To be published.

Macromolecule Content

Total Structure Weight: 80.28 kDa
Atom Count: 6,233
Modeled Residue Count: 639
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	321	Gloeophyllum trabeum ATCC 11539	Mutation(s): 0 Gene Names: GLOTRDRAFT_138785 EC: 3.2.1.8
UniProt
Find proteins for S7Q6I2 (Gloeophyllum trabeum (strain ATCC 11539 / FP-39264 / Madison 617)) Explore S7Q6I2 Go to UniProtKB: S7Q6I2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S7Q6I2
Glycosylation
Glycosylation Sites: 4	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	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	C	8		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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	D	9		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G37135JQ GlyCosmos: G37135JQ GlyGen: G37135JQ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-2)-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: G73089AB GlyCosmos: G73089AB GlyGen: G73089AB

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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	G	8		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G48018RF GlyCosmos: G48018RF GlyGen: G48018RF

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	2		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	M [auth A], N [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	J [auth A], T [auth B], U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	L [auth A], X [auth B], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain L [auth A] Focus chain X [auth B] Focus chain Y [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] 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 Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] 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 Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] 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 Z [auth B]	AA [auth B] BA [auth B] O [auth A] P [auth A] Q [auth A] AA [auth B], BA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain W [auth B] MOL2 format, chain W [auth B] mmCIF format, chain W [auth B]	W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain W [auth B] Interactions & Density Focus chain W [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain V [auth B] MOL2 format, chain K [auth A] MOL2 format, chain V [auth B] mmCIF format, chain K [auth A] mmCIF format, chain V [auth B]	K [auth A], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain V [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth B] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B] mmCIF format, chain I [auth A] mmCIF format, chain S [auth B]	I [auth A], S [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain I [auth A] Focus chain S [auth B] Interactions & Density Focus chain I [auth A] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.204 (Depositor), 0.200 (DCC)
R-Value Work: 0.154 (Depositor), 0.150 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.414	α = 90
b = 99.345	β = 90
c = 147.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-11
Type: Initial release
Version 1.1: 2015-04-01
Changes: Atomic model
Version 1.2: 2015-04-22
Changes: Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary