9SO3 | pdb_00009so3

Glucose/ xylose isomerase under 125 MPa with xylose

PDB DOI: https://doi.org/10.2210/pdb9SO3/pdb

Classification: ISOMERASE
Organism(s): Streptomyces pseudogriseolus
Mutation(s): No

Deposited: 2025-09-11 Released: 2026-09-30
Deposition Author(s): Klonecka, A., Slawek, J., Kurpiewska, K., Taube, M., Janicki, M., Kozak, M.
Funding Organization(s): Polish National Science Centre, Ministry of Science and Higher Education (Poland)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.162 (Depositor), 0.163 (DCC)
R-Value Work:
0.133 (Depositor), 0.134 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Glucose/ xylose isomerase under 125 MPa with xylose

Klonecka, A., Slawek, J., Kurpiewska, K., Taube, M., Janicki, M., Kozak, M.

To be published.

Macromolecule Content

Total Structure Weight: 43.71 kDa
Atom Count: 3,991
Modeled Residue Count: 386
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces pseudogriseolus	Mutation(s): 0 EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces pseudogriseolus) Explore P24300 Go to UniProtKB: P24300
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24300
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XLS (Subject of Investigation/LOI) Query on XLS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	D-xylose C₅ H₁₀ O₅ PYMYPHUHKUWMLA-VPENINKCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]