6FMS

IMISX-EP of Se-LspA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

In situ serial crystallography for rapid de novo membrane protein structure determination.

Huang, C.Y.Olieric, V.Howe, N.Warshamanage, R.Weinert, T.Panepucci, E.Vogeley, L.Basu, S.Diederichs, K.Caffrey, M.Wang, M.

(2018) Commun Biol 1: 124-124

  • DOI: 10.1038/s42003-018-0123-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crysta ...

    De novo membrane protein structure determination is often limited by the availability of large crystals and the difficulties in obtaining accurate diffraction data for experimental phasing. Here we present a method that combines in situ serial crystallography with de novo phasing for fast, efficient membrane protein structure determination. The method enables systematic diffraction screening and rapid data collection from hundreds of microcrystals in in meso crystallization wells without the need for direct crystal harvesting. The requisite data quality for experimental phasing is achieved by accumulating diffraction signals from isomorphous crystals identified post-data collection. The method works in all experimental phasing scenarios and is particularly attractive with fragile, weakly diffracting microcrystals. The automated serial data collection approach can be readily adopted at most microfocus macromolecular crystallography beamlines.


    Organizational Affiliation

    Swiss Light Source, Paul Scherrer Institute, CH-5232, Villigen, Switzerland. meitian.wang@psi.ch.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein signal peptidase
A, B, C, D
188Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lspAlsPA4559
EC: 3.4.23.36
Find proteins for Q9HVM5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HVM5
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Globomycin
E, F, G, H
5synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download CCD File 
A, B, C, D, E, F, G, H
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002257
Query on PRD_002257
E, F, G, HGlobomycin

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Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
ALO
Query on ALO
A,B,C,D, E,F,G,H
L-PEPTIDE LINKINGC4 H9 N O3THR
IIL
Query on IIL
A,B,C,D, E,F,G,H
L-PEPTIDE LINKINGC6 H13 N O2ILE
MLE
Query on MLE
A,B,C,D, E,F,G,H
L-PEPTIDE LINKINGC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.75α = 90
b = 110.13β = 97.08
c = 85.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDEphasing
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science Foundation IrelandIreland16/IA/4435
European UnionSwitzerland701647

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2019-06-19
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-09-04
    Changes: Data collection, Structure summary