9I79 | pdb_00009i79

Xylose Isomerase collected at 20C using time-resolved serial synchrotron crystallography with Glucose at 180 seconds

PDB DOI: https://doi.org/10.2210/pdb9I79/pdb

Classification: ISOMERASE
Organism(s): Streptomyces pseudogriseolus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-31 Released: 2026-02-18
Deposition Author(s): Schulz, E.C., Prester, A., Stetten, D.V., Gore, G., Hatton, C.E., Bartels, K., Leimkohl, J.P., Schikora, H., Ginn, H.M., TellKamp, F., Mehrabi, P.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC), German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.212 (Depositor), 0.212 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.174 (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

Xylose Isomerase collected at 20C using time-resolved serial synchrotron crystallography with Glucose at 180 seconds

Schulz, E.C., Prester, A., Stetten, D.V., Gore, G., Hatton, C.E., Bartels, K., Leimkohl, J.P., Schikora, H., Ginn, H.M., TellKamp, F., Mehrabi, P.

To be published.

Macromolecule Content

Total Structure Weight: 43.72 kDa
Atom Count: 3,609
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 Gene Names: xylA 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLO (Subject of Investigation/LOI) Query on GLO 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]	D-glucose C₆ H₁₂ O₆ GZCGUPFRVQAUEE-SLPGGIOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GLC (Subject of Investigation/LOI) Query on GLC 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]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.212 (Depositor), 0.212 (DCC)
R-Value Work: 0.172 (Depositor), 0.172 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.2	α = 90
b = 103.05	β = 90
c = 99.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	451079909
German Research Foundation (DFG)	Germany	458246365
European Research Council (ERC)	European Union	101071843
German Research Foundation (DFG)	Germany	194651731
German Federal Ministry for Education and Research	Germany	05k16gu1
German Federal Ministry for Education and Research	Germany	05k22gu6