Crystal structure of cytokinin-specific binding protein in complex with cytokinin and Ta6Br12

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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MAD phasing using the (Ta(6)Br(12))(2+) cluster: a retrospective study

Pasternak, O.Bujacz, A.Biesiadka, J.Bujacz, G.Sikorski, M.Jaskolski, M.

(2008) Acta Crystallogr D Biol Crystallogr 64: 595-606

  • DOI: https://doi.org/10.1107/S0907444908007853
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of cytokinin-specific binding protein (CSBP) containing four independent molecules with 4 x 155 = 620 residues in the asymmetric unit of the P6(4) unit cell has been solved by three-wavelength MAD using 1.8 angstroms resolution data recorded from a crystal derivatized with the dodecabromohexatantalum cation (Ta6Br12)2+. The diffraction data contained a very strong anomalous signal (allowing successful phasing even using peak SAD data alone) despite the fact that the five (Ta6Br12)2+ clusters found in the asymmetric unit have low occupancy (about 0.3). The derivative structure has been successfully refined to R = 0.158, providing interesting details on the geometry of the (Ta6Br12)2+ cluster, its interactions with the protein and on the backsoaking of a cytokinin ligand that was originally part of a CSBP-cytokinin complex in the native crystals used for (Ta6Br12)2+ derivatization. A simulation analysis of the phasing power of the (Ta6Br12)2+ ions at artificially imposed resolution limits shows that it is not possible to resolve the individual Ta atoms if the dmin limit of the data is higher than 2.9 angstroms. Additionally, for successful Ta identification the (Ta6Br12)2+ complex should be specifically bound and ordered. Good binding at the protein surface is facilitated by the presence of acidic groups, indicating higher pH buffer conditions to be preferable. In addition, the water channels in the crystal should be sufficiently wide (at least 11 angstroms) to allow free diffusion of the (Ta6Br12)2+ ions on soaking. A retrospective look at the initial molecular-replacement calculations provides interesting insights into how the peculiar packing mode and strong bias of the molecular-replacement-phased electron-density maps had hindered successful solution of the structure by this method.

  • Organizational Affiliation

    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokinin-specific binding protein
A, B, C, D
155Vigna radiataMutation(s): 0 
Gene Names: VrCSBP
Find proteins for A0A1S3THR8 (Vigna radiata var. radiata)
Explore A0A1S3THR8 
Go to UniProtKB:  A0A1S3THR8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S3THR8
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TBR

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
N [auth C],
O [auth C],
R [auth D]
Br12 Ta6
Query on EPE

Download Ideal Coordinates CCD File 
C8 H18 N2 O4 S
Query on ZEA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
L [auth B]
P [auth D]
E [auth A],
F [auth A],
K [auth B],
L [auth B],
P [auth D],
Q [auth D]
C10 H13 N5 O
Query on NA

Download Ideal Coordinates CCD File 
J [auth B],
M [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.219α = 90
b = 113.219β = 90
c = 85.077γ = 120
Software Package:
Software NamePurpose
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations