1N82

The high-resolution crystal structure of IXT6, a thermophilic, intracellular xylanase from G. stearothermophilus

PDB DOI: https://doi.org/10.2210/pdb1N82/pdb

Classification: HYDROLASE
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2002-11-19 Released: 2003-11-25
Deposition Author(s): Solomon, V., Teplitsky, A., Golan, G., Gilboa, R., Reiland, V., Shulami, S., Moryles, S., Zolotnitsky, G., Shoham, Y., Shoham, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.194
R-Value Work: 0.159

Starting Model: other
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

The high-resolution crystal structure of IXT6, a thermophilic, intracellular xylanase from G. stearothermophilus

Solomon, V., Teplitsky, A., Golan, G., Gilboa, R., Reiland, V., Shulami, S., Moryles, S., Zolotnitsky, G., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 78.73 kDa
Atom Count: 6,096
Modelled Residue Count: 658
Deposited Residue Count: 662
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
intra-cellular xylanase	A, B	331	Geobacillus stearothermophilus	Mutation(s): 0 Gene Names: XYNA EC: 3.2.1.8
UniProt
Find proteins for Q09LY9 (Geobacillus stearothermophilus) Explore Q09LY9 Go to UniProtKB: Q09LY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09LY9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain M [auth B]	C [auth A], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.194
R-Value Work: 0.159
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.481	α = 90
b = 80.579	β = 91.89
c = 79.054	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-11-25
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Refinement description
Version 1.5: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-04-03
Changes: Refinement description