5D59

In meso X-ray crystallography structure of the PepTSt-Ala-Phe complex at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.

Huang, C.Y.Olieric, V.Ma, P.Howe, N.Vogeley, L.Liu, X.Warshamanage, R.Weinert, T.Panepucci, E.Kobilka, B.Diederichs, K.Wang, M.Caffrey, M.

(2016) Acta Crystallogr D Struct Biol 72: 93-112

  • DOI: 10.1107/S2059798315021683
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase for in situ diffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically ...

    Here, a method for presenting crystals of soluble and membrane proteins growing in the lipid cubic or sponge phase for in situ diffraction data collection at cryogenic temperatures is introduced. The method dispenses with the need for the technically demanding and inefficient crystal-harvesting step that is an integral part of the lipid cubic phase or in meso method of growing crystals. Crystals are dispersed in a bolus of mesophase sandwiched between thin plastic windows. The bolus contains tens to hundreds of crystals, visible with an in-line microscope at macromolecular crystallography synchrotron beamlines and suitably disposed for conventional or serial crystallographic data collection. Wells containing the crystal-laden boluses are removed individually from hermetically sealed glass plates in which crystallization occurs, affixed to pins on goniometer bases and excess precipitant is removed from around the mesophase. The wells are snap-cooled in liquid nitrogen, stored and shipped in Dewars, and manually or robotically mounted on a goniometer in a cryostream for diffraction data collection at 100 K, as is performed routinely with standard, loop-harvested crystals. The method is a variant on the recently introduced in meso in situ serial crystallography (IMISX) method that enables crystallographic measurements at cryogenic temperatures where crystal lifetimes are enormously enhanced whilst reducing protein consumption dramatically. The new approach has been used to generate high-resolution crystal structures of a G-protein-coupled receptor, α-helical and β-barrel transporters and an enzyme as model integral membrane proteins. Insulin and lysozyme were used as test soluble proteins. The quality of the data that can be generated by this method was attested to by performing sulfur and bromine SAD phasing with two of the test proteins.


    Organizational Affiliation

    Membrane Structural and Functional Biology Group, School of Medicine and School of Biochemistry and Immunology, Trinity College, Dublin 2, D02 R590, Ireland.,Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland.,School of Medicine, Tsinghua University, Beijing 100084, People's Republic of China.,Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Di-or tripeptide:H+ symporter
A
483Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311)Mutation(s): 0 
Gene Names: dtpT
Find proteins for Q5M4H8 (Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311))
Go to UniProtKB:  Q5M4H8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78M
Query on 78M

Download SDF File 
Download CCD File 
A
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PE5
Query on PE5

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Download CCD File 
A
3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, POLYETHYLENE GLYCOL PEG400
C18 H38 O9
CUDPPTPIUWYGFI-UHFFFAOYSA-N
 Ligand Interaction
PHE
Query on PHE

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Download CCD File 
A
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
ALA
Query on ALA

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Download CCD File 
A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.570α = 90.00
b = 110.250β = 90.00
c = 110.340γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland12/IA/1255

Revision History 

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references