6DD6

Crystal structure of bacterial (6-4) photolyase PhrB from in situ serial Laue diffraction

  • Classification: LYASE
  • Organism(s): Agrobacterium tumefaciens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-05-09 Released: 2018-07-18 
  • Deposition Author(s): Ren, Z.
  • Funding Organization(s): National Institutes of Health/National Eye Institute (NIH/NEI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal-on-crystal chips for in situ serial diffraction at room temperature.

Ren, Z.Ayhan, M.Bandara, S.Bowatte, K.Kumarapperuma, I.Gunawardana, S.Shin, H.Wang, C.Zeng, X.Yang, X.

(2018) Lab Chip 18: 2246-2256

  • DOI: https://doi.org/10.1039/c8lc00489g
  • Primary Citation of Related Structures:  
    6DD6, 6DD7

  • PubMed Abstract: 

    Recent developments in serial crystallography at X-ray free electron lasers (XFELs) and synchrotrons have been driven by two scientific goals in structural biology - first, static structure determination from nano or microcrystals of membrane proteins and large complexes that are difficult for conventional cryocrystallography, and second, direct observations of transient structural species in biochemical reactions at near atomic resolution. Since room-temperature diffraction experiments naturally demand a large quantity of purified protein, sample economy is critically important for all steps of serial crystallography from crystallization, crystal delivery to data collection. Here we report the development and applications of "crystal-on-crystal" devices to facilitate large-scale in situ serial diffraction experiments on protein crystals of all sizes - large, small, or microscopic. We show that the monocrystalline quartz as a substrate material prevents vapor loss during crystallization and significantly reduces background X-ray scattering. These devices can be readily adopted at XFEL and synchrotron beamlines, which enable efficient delivery of hundreds to millions of crystals to the X-ray beam, with an overall protein consumption per dataset comparable to that of cryocrystallography.


  • Organizational Affiliation

    Department of Chemistry, The University of Illinois at Chicago, Chicago, IL 60607, USA. zren@uic.edu xiaojing@uic.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photolyase PhrB518Agrobacterium tumefaciensMutation(s): 0 
Gene Names: SY94_4724
EC: 4.1.99.13
UniProt
Find proteins for A9CH39 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore A9CH39 
Go to UniProtKB:  A9CH39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9CH39
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.7α = 90
b = 106.8β = 90
c = 57.3γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Precognitiondata reduction
Epinormdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2018-07-18 
  • Deposition Author(s): Ren, Z.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR01EY024363

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description