8PXJ | pdb_00008pxj

Structure of Whitewater Arroyo virus GP1 glycoprotein, solved at wavelength 2.75 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.276 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.251 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8PXJ

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.

El Omari, K.Duman, R.Mykhaylyk, V.Orr, C.M.Latimer-Smith, M.Winter, G.Grama, V.Qu, F.Bountra, K.Kwong, H.S.Romano, M.Reis, R.I.Vogeley, L.Vecchia, L.Owen, C.D.Wittmann, S.Renner, M.Senda, M.Matsugaki, N.Kawano, Y.Bowden, T.A.Moraes, I.Grimes, J.M.Mancini, E.J.Walsh, M.A.Guzzo, C.R.Owens, R.J.Jones, E.Y.Brown, D.G.Stuart, D.I.Beis, K.Wagner, A.

(2023) Commun Chem 6: 219-219

  • DOI: https://doi.org/10.1038/s42004-023-01014-0
  • Primary Citation Related Structures: 
    8PWN, 8PX0, 8PX1, 8PX4, 8PX5, 8PX7, 8PX9, 8PXC, 8PXG, 8PXH, 8PXJ, 8PXK, 8PXL, 8PYV, 8PYZ, 8PZ4, 8PZ5

  • PubMed Abstract: 

    Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.


  • Organizational Affiliation
    • Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.

Macromolecule Content 

  • Total Structure Weight: 20.18 kDa 
  • Atom Count: 1,218 
  • Modeled Residue Count: 146 
  • Deposited Residue Count: 165 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycoprotein G1165Mammarenavirus whitewaterenseMutation(s): 0 
Gene Names: GPCGP-C
UniProt
Find proteins for Q911P0 (Whitewater Arroyo mammarenavirus (isolate Rat/United States/AV 9310135/1995))
Explore Q911P0 
Go to UniProtKB:  Q911P0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ911P0
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CD

Query on CD



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.276 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.83α = 90
b = 106.83β = 90
c = 74.86γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Diamond Light SourceUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary