5UVI

Serial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.248 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation.

Martin-Garcia, J.M.Conrad, C.E.Nelson, G.Stander, N.Zatsepin, N.A.Zook, J.Zhu, L.Geiger, J.Chun, E.Kissick, D.Hilgart, M.C.Ogata, C.Ishchenko, A.Nagaratnam, N.Roy-Chowdhury, S.Coe, J.Subramanian, G.Schaffer, A.James, D.Ketwala, G.Venugopalan, N.Xu, S.Corcoran, S.Ferguson, D.Weierstall, U.Spence, J.C.H.Cherezov, V.Fromme, P.Fischetti, R.F.Liu, W.

(2017) IUCrJ 4: 439-454

  • DOI: 10.1107/S205225251700570X
  • Primary Citation of Related Structures:  
    5UVI, 5UVK, 5UVJ, 5UVL

  • PubMed Abstract: 
  • Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also ...

    Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5-20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2A AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2A AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2A AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5-20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.


    Organizational Affiliation

    School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2aA447Homo sapiensEscherichia coliMutation(s): 3 
Gene Names: ADORA2AADORA2cybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for P29274 (Homo sapiens)
Explore P29274 
Go to UniProtKB:  P29274
PHAROS:  P29274
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
F [auth A], G [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZMA (Subject of Investigation/LOI)
Query on ZMA

Download Ideal Coordinates CCD File 
B [auth A]4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol
C16 H15 N7 O2
PWTBZOIUWZOPFT-UHFFFAOYSA-N
 Ligand Interaction
OLA (Subject of Investigation/LOI)
Query on OLA

Download Ideal Coordinates CCD File 
H [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZMA BindingDB:  5UVI Ki: min: 0.1, max: 64 (nM) from 16 assay(s)
Kd: 0.22 (nM) from 1 assay(s)
IC50: min: 0.68, max: 81 (nM) from 7 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.3α = 90
b = 180.3β = 90
c = 142.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cheetahdata collection
CrystFELdata scaling
CrystFELdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Flinn FoundationUnited States1991
STC Program of the National Science Foundation through BioXFELUnited States1231306
National Institute of Health Femtosecond Nano-crystallography of Membrane ProteinsUnited StatesR01GM095583
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108635
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54GM094618
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesY1-CO-1020
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesY1-GM-1104
Department of Energy (DOE, United States)United StatesDE-AC02-06CH1135

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence