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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
D [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
DLZ
Query on DLZ

Download Ideal Coordinates CCD File 
C [auth A]1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
C13 H18 N4 O6
SXDXRJZUAJBNFL-XKSSXDPKSA-N
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

View Full Validation Report



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