5OSN

Crystal Structure of Bovine Enterovirus 2 determined with Serial Femtosecond X-ray Crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.4 of the entry. See complete history


Literature

High-speed fixed-target serial virus crystallography.

Roedig, P.Ginn, H.M.Pakendorf, T.Sutton, G.Harlos, K.Walter, T.S.Meyer, J.Fischer, P.Duman, R.Vartiainen, I.Reime, B.Warmer, M.Brewster, A.S.Young, I.D.Michels-Clark, T.Sauter, N.K.Kotecha, A.Kelly, J.Rowlands, D.J.Sikorsky, M.Nelson, S.Damiani, D.S.Alonso-Mori, R.Ren, J.Fry, E.E.David, C.Stuart, D.I.Wagner, A.Meents, A.

(2017) Nat Methods 14: 805-810

  • DOI: https://doi.org/10.1038/nmeth.4335
  • Primary Citation of Related Structures:  
    5MQW, 5OSN

  • PubMed Abstract: 

    We report a method for serial X-ray crystallography at X-ray free-electron lasers (XFELs), which allows for full use of the current 120-Hz repetition rate of the Linear Coherent Light Source (LCLS). Using a micropatterned silicon chip in combination with the high-speed Roadrunner goniometer for sample delivery, we were able to determine the crystal structures of the picornavirus bovine enterovirus 2 (BEV2) and the cytoplasmic polyhedrosis virus type 18 polyhedrin, with total data collection times of less than 14 and 10 min, respectively. Our method requires only micrograms of sample and should therefore broaden the applicability of serial femtosecond crystallography to challenging projects for which only limited sample amounts are available. By synchronizing the sample exchange to the XFEL repetition rate, our method allows for most efficient use of the limited beam time available at XFELs and should enable a substantial increase in sample throughput at these facilities.


  • Organizational Affiliation

    Photon Science, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein275Enterovirus EMutation(s): 0 
UniProt
Find proteins for Q65480 (Enterovirus E)
Explore Q65480 
Go to UniProtKB:  Q65480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65480
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein244Enterovirus EMutation(s): 0 
UniProt
Find proteins for Q65480 (Enterovirus E)
Explore Q65480 
Go to UniProtKB:  Q65480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65480
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein243Enterovirus EMutation(s): 0 
UniProt
Find proteins for Q65480 (Enterovirus E)
Explore Q65480 
Go to UniProtKB:  Q65480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65480
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein71Enterovirus EMutation(s): 0 
UniProt
Find proteins for Q65480 (Enterovirus E)
Explore Q65480 
Go to UniProtKB:  Q65480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65480
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPH
Query on SPH

Download Ideal Coordinates CCD File 
E [auth A]SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
OSF
Query on OSF

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J [auth C]octyl sulfate
C8 H17 O4 S
UZZYXUGECOQHPU-UHFFFAOYSA-M
GLU
Query on GLU

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H [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
SO4
Query on SO4

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K [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 436.6α = 90
b = 436.6β = 90
c = 436.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Data collection, Database references
  • Version 2.0: 2018-10-03
    Changes: Atomic model, Data collection, Derived calculations, Refinement description
  • Version 2.1: 2018-10-10
    Changes: Data collection, Structure summary
  • Version 2.2: 2018-11-14
    Changes: Data collection, Structure summary
  • Version 2.3: 2019-07-31
    Changes: Data collection, Refinement description
  • Version 2.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description