4ZB5 | pdb_00004zb5

A form of glucose isomerase collected at 100K.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.154 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.115 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 
    0.117 (Depositor) 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 
    • Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xylose isomerase388Streptomyces rubiginosusMutation(s): 0 
Gene Names: xylA
EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus)
Explore P24300 
Go to UniProtKB:  P24300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24300
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.154 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.115 (Depositor), 0.120 (DCC) 
  • R-Value Observed: 0.117 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.904α = 90
b = 98.152β = 90
c = 102.704γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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