4TTN | pdb_00004ttn

Quasi-racemic structure of [G6A]kalata B1

• PDB DOI: https://doi.org/10.2210/pdb4TTN/pdb

• Classification: PLANT PROTEIN
• Organism(s): Oldenlandia affinis, synthetic construct
• Mutation(s): Yes 


• Deposited: 2014-06-22 Released: 2014-09-10 
• Deposition Author(s): Wang, C.K., King, G.J., Craik, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Racemic and Quasi-Racemic X-ray Structures of Cyclic Disulfide-Rich Peptide Drug Scaffolds.

Wang, C.K., King, G.J., Northfield, S.E., Ojeda, P.G., Craik, D.J.

(2014) Angew Chem Int Ed Engl 53: 11236-11241

• PubMed: 25168664 
• DOI: https://doi.org/10.1002/anie.201406563
• Primary Citation Related Structures: 
  4TTK, 4TTL, 4TTM, 4TTN, 4TTO


• PubMed Abstract: 
  

  Cyclic disulfide-rich peptides have exceptional stability and are promising frameworks for drug design. We were interested in obtaining X-ray structures of these peptides to assist in drug design applications, but disulfide-rich peptides can be notoriously difficult to crystallize. To overcome this limitation, we chemically synthesized the L- and D-forms of three prototypic cyclic disulfide-rich peptides: SFTI-1 (14-mer with one disulfide bond), cVc1.1 (22-mer with two disulfide bonds), and kB1 (29-mer with three disulfide bonds) for racemic crystallization studies. Facile crystal formation occurred from a racemic mixture of each peptide, giving structures solved at resolutions from 1.25 Å to 1.9 Å. Additionally, we obtained the quasi-racemic structures of two mutants of kB1, [G6A]kB1, and [V25A]kB1, which were solved at a resolution of 1.25 Å and 2.3 Å, respectively. The racemic crystallography approach appears to have broad utility in the structural biology of cyclic peptides.

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Organizational Affiliation: 
• Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072 (Australia).

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 5.97 kDa 
• Atom Count: 492 
• Modeled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kalata-B1	A	29	Oldenlandia affinis	Mutation(s): 1
UniProt
Find proteins for P56254 (Oldenlandia affinis) Explore P56254  Go to UniProtKB:  P56254

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-kalata B1	B	29	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.186	α = 93.8
b = 25.923	β = 106.59
c = 37.713	γ = 99.91

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Wang, C.K., King, G.J., Craik, D.J.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.4: 2024-10-30
  Changes: Structure summary