5LBR

Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography.

Edlund, P.Takala, H.Claesson, E.Henry, L.Dods, R.Lehtivuori, H.Panman, M.Pande, K.White, T.Nakane, T.Berntsson, O.Gustavsson, E.Bath, P.Modi, V.Roy-Chowdhury, S.Zook, J.Berntsen, P.Pandey, S.Poudyal, I.Tenboer, J.Kupitz, C.Barty, A.Fromme, P.Koralek, J.D.Tanaka, T.Spence, J.Liang, M.Hunter, M.S.Boutet, S.Nango, E.Moffat, K.Groenhof, G.Ihalainen, J.Stojkovic, E.A.Schmidt, M.Westenhoff, S.

(2016) Sci Rep 6: 35279-35279

  • DOI: https://doi.org/10.1038/srep35279
  • Primary Citation of Related Structures:  
    5K5B, 5L8M, 5LBR

  • PubMed Abstract: 

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.


  • Organizational Affiliation

    Australian Research Council Centre of Excellence for Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, 3086 Melbourne, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriophytochrome343Deinococcus radioduransMutation(s): 0 
Gene Names: bphPDR_A0050
EC: 2.7.13.3
UniProt
Find proteins for Q9RZA4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RZA4 
Go to UniProtKB:  Q9RZA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RZA4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LBV
Query on LBV

Download Ideal Coordinates CCD File 
B [auth A]3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid
C33 H37 N4 O6
DKMLMZVDTGOEGU-ISEYCTJISA-O
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.22α = 90
b = 55.49β = 92.84
c = 71.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
PHASERphasing
CrystFELdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Data collection
  • Version 1.2: 2018-11-14
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-01-10
    Changes: Refinement description