5MG1

Structure of the photosensory module of Deinococcus phytochrome by serial femtosecond X-ray crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers.

Fuller, F.D.Gul, S.Chatterjee, R.Burgie, E.S.Young, I.D.Lebrette, H.Srinivas, V.Brewster, A.S.Michels-Clark, T.Clinger, J.A.Andi, B.Ibrahim, M.Pastor, E.de Lichtenberg, C.Hussein, R.Pollock, C.J.Zhang, M.Stan, C.A.Kroll, T.Fransson, T.Weninger, C.Kubin, M.Aller, P.Lassalle, L.Brauer, P.Miller, M.D.Amin, M.Koroidov, S.Roessler, C.G.Allaire, M.Sierra, R.G.Docker, P.T.Glownia, J.M.Nelson, S.Koglin, J.E.Zhu, D.Chollet, M.Song, S.Lemke, H.Liang, M.Sokaras, D.Alonso-Mori, R.Zouni, A.Messinger, J.Bergmann, U.Boal, A.K.Bollinger, J.M.Krebs, C.Hogbom, M.Phillips, G.N.Vierstra, R.D.Sauter, N.K.Orville, A.M.Kern, J.Yachandra, V.K.Yano, J.

(2017) Nat Methods 14: 443-449

  • DOI: https://doi.org/10.1038/nmeth.4195
  • Primary Citation of Related Structures:  
    5MG0, 5MG1

  • PubMed Abstract: 

    X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.


  • Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriophytochrome524Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.7α = 90
b = 151.7β = 90
c = 151.2γ = 120
Software Package:
Software NamePurpose
cctbx.xfeldata collection
cctbx.primedata reduction
cctbx.xfeldata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
psanadata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science FoundationUnited StatesMCB-1329956

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-15
    Changes: Database references
  • Version 1.2: 2017-04-12
    Changes: Database references
  • Version 1.3: 2018-11-14
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2024-10-09
    Changes: Structure summary