6IRK

Crystal structure of glucose isomerase by fixed-target serial femtosecond crystallography

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

  • Deposited: 2018-11-13 Released: 2019-05-22 
  • Deposition Author(s): Nam, K.H.
  • Funding Organization(s): National Research Foundation (Korea)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Nylon mesh-based sample holder for fixed-target serial femtosecond crystallography.

Lee, D., Baek, S., Park, J., Lee, K., Kim, J., Lee, S.J., Chung, W.K., Lee, J.L., Cho, Y., Nam, K.H.

(2019) Sci Rep 9: 6971-6971

  • DOI: https://doi.org/10.1038/s41598-019-43485-z
  • Primary Citation of Related Structures:  
    6IRJ, 6IRK

  • PubMed Abstract: 

    • Fixed-target serial femtosecond crystallography (FT-SFX) was an important advance in crystallography by dramatically reducing sample consumption, while maintaining the benefits of SFX for obtaining crystal structures at room temperature without radiation damage ...

    Fixed-target serial femtosecond crystallography (FT-SFX) was an important advance in crystallography by dramatically reducing sample consumption, while maintaining the benefits of SFX for obtaining crystal structures at room temperature without radiation damage. Despite a number of advantages, preparation of a sample holder for the sample delivery in FT-SFX with the use of many crystals in a single mount at ambient temperature is challenging as it can be complicated and costly, and thus, development of an efficient sample holder is essential. In this study, we introduced a nylon mesh-based sample holder enclosed by a polyimide film. This sample holder can be rapidly manufactured using a commercially available nylon mesh with pores of a desired size at a low cost without challenging technology. Furthermore, this simple device is highly efficient in data acquisition. We performed FT-SFX using a nylon mesh-based sample holder and collected over 130,000 images on a single sample holder using a 30 Hz X-ray pulse for 1.2 h. We determined the crystal structures of lysozyme and glucose isomerase using the nylon mesh at 1.65 and 1.75 Å, respectively. The nylon mesh exposed to X-rays produced very low levels of background scattering at 3.75 and 4.30 Å, which are negligible for data analysis. Our method provides a simple and rapid but highly efficient way to deliver samples for FT-SFX.

    Organizational Affiliation: 

    Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea. structures@korea.ac.kr.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.05α = 90
b = 99β = 90
c = 101.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2019-05-22 
    • Deposition Author(s): Nam, K.H.
Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1D1A1B03033087
National Research Foundation (Korea)Korea, Republic Of2017M3A9F6029736

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection
  • Version 1.2: 2019-08-28
    Changes: Data collection
  • Version 1.3: 2019-09-18
    Changes: Data collection
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations