1YBK

RHCC cocrystallized with CAPB

• PDB DOI: https://doi.org/10.2210/pdb1YBK/pdb

• Classification: PROTEIN BINDING
• Organism(s): Staphylothermus marinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-21 Released: 2005-01-18 
• Deposition Author(s): Stetefeld, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Favourable mediation of crystal contacts by cocoamidopropylbetaine (CAPB).

Ozbek, S., Muller, J.F., Figgemeier, E., Stetefeld, J.

(2005) Acta Crystallogr D Biol Crystallogr 61: 477-480

• PubMed: 15805603 
• DOI: https://doi.org/10.1107/S0907444905001204
• Primary Citation of Related Structures:  
  1YBK


• PubMed Abstract: 
  

  Crystals of excellent quality are a prerequisite for high-resolution X-ray data. However, in refinement protocols of crystallization conditions it is often difficult to obtain the right combination of, for example, protein concentration, drop size, temperature and additives. A novel approach for optimizing crystal contacts in a most favourable fashion by performing crystallization setups with the zwitterionic surfactant cocoamidoproylbetaine (CAPB) is introduced. In the presence of this surfactant, highly diffracting crystals were obtained. Here, data from a right-handed coiled coil (RHCC) in complex with CAPB at 1.4 A resolution are presented. The addition of CAPB using otherwise identical crystallization conditions and the same X-ray source caused an improvement in resolution from 2.9 to 1.4 A.

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Organizational Affiliation: 

Department of Biophysical Chemistry, Biozentrum, University of Basel, Klingelbergstrase 70, CH-4056 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 24.23 kDa 
• Atom Count: 2,135 
• Modelled Residue Count: 205 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tetrabrachion	A, B, C, D	52	Staphylothermus marinus	Mutation(s): 0
UniProt
Find proteins for Q54436 (Staphylothermus marinus) Explore Q54436  Go to UniProtKB:  Q54436

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEQ	G [auth C]	N-(CARBOXYMETHYL)-N,N-DIMETHYL-3-[(1-OXODODECYL)AMINO]-1-PROPANAMINIUM INNER SALT C19 H38 N2 O3 MRUAUOIMASANKQ-UHFFFAOYSA-N
SO4	E [auth A], F [auth B], H [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.811	α = 90
b = 110.811	β = 90
c = 71.121	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Stetefeld, J.

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary