7DMM | pdb_00007dmm

Structure of a glucose isomerase crystal grown in an aqueous glycerol solution without any precipitants

• PDB DOI: https://doi.org/10.2210/pdb7DMM/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces pseudogriseolus
• Mutation(s): Yes 


• Deposited: 2020-12-04 Released: 2021-12-08 
• Deposition Author(s): Suzuki, Y., Maita, N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Extraordinarily fast growth of high-quality glucose isomerase crystals simply by concentration in a precipitant-free solution with a cryoprotectant

Suzuki, Y., Ikemitsu, N., Maita, N.

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 PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 43.4 kDa 
• Atom Count: 3,460 
• Modeled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	386	Streptomyces pseudogriseolus	Mutation(s): 1  EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	E [auth A], F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.99 Å
• R-Value Free:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.61	α = 90
b = 98.46	β = 90
c = 102.3	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Suzuki, Y., Maita, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K04960

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description