9GRD

Cryo-electron microscopy structure of glucose/xylose isomerase from Streptomyces rubiginosus with cobalt ions in the active site

• PDB DOI: https://doi.org/10.2210/pdb9GRD/pdb
• EM Map EMD-51521: EMDB EMDataResource

• Classification: METAL BINDING PROTEIN
• Organism(s): Streptomyces rubiginosus
• Mutation(s): No 


• Deposited: 2024-09-11 Released: 2024-10-02 
• Deposition Author(s): Slawek, J., Klonecka, A., Rawski, M., Kozak, M.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.99 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-electron microscopy structure of glucose/xylose isomerase from Streptomyces rubiginosus with cobalt ions in the active site

Slawek, J., Klonecka, A., Kozak, M., Rawski, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 173.6 kDa 
• Atom Count: 12,196 
• Modelled Residue Count: 1,548 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A, B, C, D	388	Streptomyces rubiginosus	Mutation(s): 0  EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.99 Å
• Aggregation State: 3D ARRAY 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Slawek, J., Klonecka, A., Rawski, M., Kozak, M.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2020/39/O/ST4/03465

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release