4US6 | pdb_00004us6

New Crystal Form of Glucose Isomerase Grown in Short Peptide Supramolecular Hydrogels

• PDB DOI: https://doi.org/10.2210/pdb4US6/pdb

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


• Deposited: 2014-07-03 Released: 2015-05-13 
• Deposition Author(s): Gavira, J.A., Conejero-Muriel, M., Diaz-Mochon, J.J., Alvarez de Cienfuegos, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.132 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.106 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.108 (Depositor) 

Starting Model: experimental

Literature

Influence of the Chirality of Short Peptide Supramolecular Hydrogels in Protein Crystallogenesis.

Conejero-Muriel, M., Gavira, J.A., Pineda-Molina, E., Belsom, A., Bradley, M., Moral, M., Garcia-Lopez Duran, J.D.D., Luque Gonzalez, A., Diaz-Mochon, J.J., Contreras-Montoya, R., Martinez-Peragon, A., Cuerva, J.M., Alvarez De Cienfuegos, L.

(2015) Chem Commun (Camb) 51: 3862

• PubMed: 25655841 
• DOI: https://doi.org/10.1039/c4cc09024a
• Primary Citation Related Structures: 
  4US6


• PubMed Abstract: 
  

  For the first time the influence of the chirality of the gel fibers in protein crystallogenesis has been studied. Enantiomeric hydrogels 1 and 2 were tested with model proteins lysozyme and glucose isomerase and a formamidase extracted from B. cereus. Crystallization behaviour and crystal quality of these proteins in both hydrogels are presented and compared.

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Organizational Affiliation: 
• Laboratorio de Estudios Cristalográficos, Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), Av. de las Palmeras 4, 18100 Armilla, Granada, Spain. [e-mail].

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: 87.32 kDa 
• Atom Count: 7,687 
• Modeled Residue Count: 773 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], I [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth A], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.132 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.106 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.108 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.999	α = 90
b = 93.677	β = 90
c = 99.215	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Gavira, J.A., Conejero-Muriel, M., Diaz-Mochon, J.J., Alvarez de Cienfuegos, L.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description