5GQE | pdb_00005gqe

Crystal structure of michaelis complex of xylanase mutant (T82A, N127S, and E128H) from Streptomyces olivaceoviridis E-86

PDB DOI: https://doi.org/10.2210/pdb5GQE/pdb

Classification: HYDROLASE
Organism(s): Streptomyces olivaceoviridis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-08-07 Released: 2017-08-09
Deposition Author(s): Suzuki, R., Fujimoto, Z., Kaneko, S., Kuno, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.249 (Depositor), 0.201 (DCC)
R-Value Work:
0.179 (Depositor), 0.198 (DCC)
R-Value Observed:
0.179 (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

Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant

Suzuki, R., Fujimoto, Z., Kaneko, S., Hasegawa, T., Kuno, A.

(2019) J Appl Glycosci (1999) 65

DOI: https://doi.org/10.5458/jag.jag.JAG-2017_011

Macromolecule Content

Total Structure Weight: 96.37 kDa
Atom Count: 7,400
Modeled Residue Count: 858
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylanase	A, B	436	Streptomyces olivaceoviridis	Mutation(s): 3 EC: 3.2.1.8
UniProt
Find proteins for Q7SI98 (Streptomyces olivaceoviridis) Explore Q7SI98 Go to UniProtKB: Q7SI98
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7SI98
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	C, F	5		N/A	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F
Glycosylation Resources
GlyTouCan: G47101GE GlyCosmos: G47101GE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	D	4		N/A	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G60650FG GlyCosmos: G60650FG

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	E, G	2		N/A	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G87728WL GlyCosmos: G87728WL

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	H	3		N/A	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G87429QT GlyCosmos: G87429QT

Biologically Interesting Molecules (External Reference)

2 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900116 Query on PRD_900116	E, G	4beta-beta-xylobiose	Oligosaccharide / Metabolism		Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117 Query on PRD_900117	H	4beta-beta-xylotriose	Oligosaccharide / Metabolism		Interactions Focus chain H Interactions & Density Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.249 (Depositor), 0.201 (DCC)
R-Value Work: 0.179 (Depositor), 0.198 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.13	α = 90
b = 94.007	β = 90
c = 137.641	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-08-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-08-09
Type: Initial release
Version 1.1: 2019-07-31
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary