1OD8 | pdb_00001od8

Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam

PDB DOI: https://doi.org/10.2210/pdb1OD8/pdb

Classification: HYDROLASE/LECTIN
Organism(s): Streptomyces lividans
Expression System: Streptomyces lividans
Mutation(s): No

Deposited: 2003-02-14 Released: 2003-04-08
Deposition Author(s): Gloster, T.M., Roberts, S., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.126 (Depositor), 0.136 (DCC)
R-Value Work:
0.103 (Depositor), 0.119 (DCC)
R-Value Observed:
0.104 (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

A Xylobiose-Derived Isofagomine Lactam Glycosidase Inhibitor Binds as its Amide Tautomer

Gloster, T.M., Williams, S.J., Tarling, C., Roberts, S., Dupont, C., Jodoin, P., Shareck, F., Withers, S.G., Davies, G.J.

(2003) Chem Commun (Camb) 8: 944

PubMed: 12744311 Search on PubMed
DOI: https://doi.org/10.1039/b301829f
Primary Citation Related Structures:
1OD8

PubMed Abstract:
The atomic-resolution structure of a xylobiose-derived isofagomine lactam in complex with the xylanase Xyn10A from Streptomyces lividans reveals that the lactam is bound to the enzyme as the amide tautomer, with "reversed" protonation-states for nucleophile and acid-base.

Organizational Affiliation

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, UK.

Macromolecule Content

Total Structure Weight: 34.89 kDa
Atom Count: 3,076
Modeled Residue Count: 302
Deposited Residue Count: 313
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE A	A	313	Streptomyces lividans	Mutation(s): 0 EC: 3.2.1.8
UniProt
Find proteins for P26514 (Streptomyces lividans) Explore P26514 Go to UniProtKB: P26514
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26514
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYP Query on XYP Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth A]	F [auth A], J [auth A]	beta-D-xylopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-KKQCNMDGSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain J [auth A]
XDL Query on XDL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A]	E [auth A], I [auth A]	XYLOSE-DERIVED ISOFAGOMINE LACTAM C₅ H₉ N O₂ RYKLZUPYJFFNRR-BYPYZUCNSA-N		Interactions Focus chain E [auth A] Focus chain I [auth A] Interactions & Density Focus chain E [auth A] Focus chain I [auth A]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain K [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain K [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.126 (Depositor), 0.136 (DCC)
R-Value Work: 0.103 (Depositor), 0.119 (DCC)
R-Value Observed: 0.104 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.814	α = 90
b = 45.878	β = 90
c = 85.737	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-04-08

Deposition Author(s):

Gloster, T.M.

Roberts, S.

Davies, G.J.

Revision History (Full details and data files)

Version 1.0: 2003-04-08
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary