4ZB5

A form of glucose isomerase collected at 100K.

• PDB DOI: https://doi.org/10.2210/pdb4ZB5/pdb

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


• Deposited: 2015-04-14 Released: 2016-03-23 
• Deposition Author(s): Sandy, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.154 
• R-Value Work: 0.115 
• R-Value Observed: 0.117 

Literature

A generic protocol for protein crystal dehydration using the HC1b humidity controller.

Lobley, C.M., Sandy, J., Sanchez-Weatherby, J., Mazzorana, M., Krojer, T., Nowak, R.P., Sorensen, T.L.

(2016) Acta Crystallogr D Struct Biol 72: 629-640

• PubMed: 27139626 
• DOI: https://doi.org/10.1107/S2059798316003065
• Primary Citation of Related Structures:  
  4ZB0, 4ZB2, 4ZB5, 4ZBC


• PubMed Abstract: 
  

  Dehydration may change the crystal lattice and affect the mosaicity, resolution and quality of X-ray diffraction data. A dehydrating environment can be generated around a crystal in several ways with various degrees of precision and complexity. This study uses a high-precision crystal humidifier/dehumidifier to provide an airstream of known relative humidity in which the crystals are mounted: a precise yet hassle-free approach to altering crystal hydration. A protocol is introduced to assess the impact of crystal dehydration systematically applied to nine experimental crystal systems. In one case, that of glucose isomerase, dehydration triggering a change of space group from I222 to P21212 was observed. This observation is supported by an extended study of the behaviour of the glucose isomerase crystal structure during crystal dehydration.

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Organizational Affiliation: 

Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.57 kDa 
• Atom Count: 3,649 
• Modelled Residue Count: 387 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	D [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-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: 2.00 Å
• R-Value Free: 0.154 
• R-Value Work: 0.115 
• R-Value Observed: 0.117 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.904	α = 90
b = 98.152	β = 90
c = 102.704	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Sandy, J.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-05-11
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary