6QUG

GHK tagged MBP-Nup98(1-29)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

The copper(II)-binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography.

Mehr, A.Henneberg, F.Chari, A.Gorlich, D.Huyton, T.

(2020) Acta Crystallogr D Struct Biol 76: 1222-1232

  • DOI: https://doi.org/10.1107/S2059798320013741
  • Primary Citation of Related Structures:  
    6QUG, 6QUH, 6QUI, 6QUJ

  • PubMed Abstract: 

    The growth of diffraction-quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high-affinity copper(II)-binding tripeptide GHK was fused to the N-terminus of a GFP variant and an MBP-FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square-pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S-atom positions could also be located in log-likelihood-gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR-SAD phasing.


  • Organizational Affiliation

    Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltodextrin-binding protein,Nucleoporin, putative
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
402Escherichia coliTetrahymena thermophila SB210
This entity is chimeric
Mutation(s): 0 
Gene Names: malENCTC8450_00456NCTC9775_03059TTHERM_00071070
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for I7MHJ5 (Tetrahymena thermophila (strain SB210))
Explore I7MHJ5 
Go to UniProtKB:  I7MHJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsI7MHJ5P0AEX9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth C],
OA [auth K],
QA [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth D],
EA [auth D],
KA [auth I],
MA [auth J]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth C]
CA [auth D]
FA [auth E]
GA [auth F]
HA [auth G]
AA [auth C],
CA [auth D],
FA [auth E],
GA [auth F],
HA [auth G],
IA [auth H],
JA [auth I],
LA [auth J],
NA [auth K],
PA [auth L],
Y [auth A],
Z [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.91α = 90
b = 286.78β = 92.01
c = 110.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2020-12-09
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 3.1: 2020-12-16
    Changes: Database references