6QUF | pdb_00006quf

Protein crystallization by ionic liquid hydrogel support: reference crystal of glucose isomerase grown on standard silanized glass

• PDB DOI: https://doi.org/10.2210/pdb6QUF/pdb

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


• Deposited: 2019-02-27 Released: 2019-03-13 
• Deposition Author(s): Belviso, B.D., Caliandro, R., Caliandro, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free: 
  0.129 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.107 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.108 (Depositor) 

Starting Model: experimental

Literature

Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes

Belviso, B.D., Caliandro, R., Salehi, S.M., di Profio, G., Caliandro, R.

(2019) Crystals (Basel) 9: 253

• DOI: https://doi.org/10.3390/cryst9050253

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)

Macromolecule Content 

• Total Structure Weight: 43.77 kDa 
• Atom Count: 3,757 
• Modeled Residue Count: 385 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

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 rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.19 Å
• R-Value Free:  0.129 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.107 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.108 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.522	α = 90
b = 98.167	β = 90
c = 101.851	γ = 90

Software Package:

Software Name	Purpose
xia2	data reduction
Aimless	data scaling
Sir2014	phasing
REFMAC	refinement
BUSTER-TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Belviso, B.D., Caliandro, R., Caliandro, R.

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection
• Version 1.2: 2019-07-10
  Changes: Data collection
• Version 1.3: 2019-09-25
  Changes: Data collection, Database references
• Version 1.4: 2020-04-08
  Changes: Database references
• Version 1.5: 2024-01-24
  Changes: Data collection, Database references, Refinement description