6VRS

Single particle reconstruction of glucose isomerase from Streptomyces rubiginosus based on data acquired in the presence of substantial aberrations

• PDB DOI: https://doi.org/10.2210/pdb6VRS/pdb
• EM Map EMD-21371: EMDB EMDataResource

• Classification: ISOMERASE
• Organism(s): Streptomyces rubiginosus
• Mutation(s): No 


• Deposited: 2020-02-09 Released: 2020-02-19 
• Deposition Author(s): Bromberg, R., Guo, Y., Borek, D., Otwinowski, Z.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

High-resolution cryo-EM reconstructions in the presence of substantial aberrations

Bromberg, R., Guo, Y., Borek, D., Otwinowski, Z.

(2020) IUCrJ 7: 445-452

• DOI: https://doi.org/10.1107/S2052252520002444

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 173.57 kDa 
• Atom Count: 12,208 
• 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
MN (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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-19 
Deposition Author(s): Bromberg, R., Guo, Y., Borek, D., Otwinowski, Z.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM117080
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM118619
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R21GM126406
Department of Energy (DOE, United States)	United States	DE-SC0019600
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-02-19
  Type: Initial release
  
• Version 1.1: 2020-05-13
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description