2C4B

Inhibitor cystine knot protein McoEeTI fused to the catalytically inactive barnase mutant H102A

• PDB DOI: https://doi.org/10.2210/pdb2C4B/pdb

• Classification: FUSION PROTEIN
• Organism(s): Bacillus amyloliquefaciens, Momordica cochinchinensis, Ecballium elaterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-18 Released: 2005-11-21 
• Deposition Author(s): Niemann, H.H., Schmoldt, H.U., Wentzel, A., Kolmar, H., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.164 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 

Starting Model: experimental

Literature

Barnase Fusion as a Tool to Determine the Crystal Structure of the Small Disulfide-Rich Protein Mcoeeti.

Niemann, H.H., Schmoldt, H.U., Wentzel, A., Kolmar, H., Heinz, D.W.

(2006) J Mol Biol 356: 1

• PubMed: 16337652 
• DOI: https://doi.org/10.1016/j.jmb.2005.11.005
• Primary Citation of Related Structures:  
  2C4B


• PubMed Abstract: 
  

  We present a fusion system suited to determine the crystal structure of small disulfide-rich proteins. McoEeTI, a hybrid inhibitor cystine knot microprotein, was produced as a soluble fusion to a catalytically inactive variant of the RNAse barnase in Escherichia coli. Functioning as a versatile tag, barnase facilitated purification, crystallization and high-resolution structure determination. Flexibility of the linker region allows for different relative orientations of barnase and the fusion partner in two crystallographically independent molecules and may thereby facilitate crystal packing. Nevertheless, the linker region is well ordered in both molecules. This system may prove more generally useful to determine the crystal structure of peptides and small proteins.

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Organizational Affiliation: 

Division of Structural Biology, German Research Centre for Biotechnology (GBF) Mascheroder Weg 1, D-38124 Braunschweig, Germany. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 35.79 kDa 
• Atom Count: 3,057 
• Modelled Residue Count: 284 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BARNASE MCOEETI FUSION	A, B	143	Bacillus amyloliquefaciens, Momordica cochinchinensis, Ecballium elaterium This entity is chimeric	Mutation(s): 1  EC: 3.1.27.3 (PDB Primary Data), 3.1.27 (UniProt)
UniProt
Find proteins for P82409 (Momordica cochinchinensis) Explore P82409  Go to UniProtKB:  P82409
Find proteins for P00648 (Bacillus amyloliquefaciens) Explore P00648  Go to UniProtKB:  P00648
Find proteins for P12071 (Ecballium elaterium) Explore P12071  Go to UniProtKB:  P12071
UniProt Groups	P82409P00648P12071

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	C [auth A], D [auth A], IA [auth B], JA [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
MES	KA [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	HA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth B], ZA [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth A], LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	AB [auth B], J [auth A], K [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
UNX	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.164 
• R-Value Work: 0.132 
• R-Value Observed: 0.133 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.02	α = 90
b = 217.71	β = 90
c = 58.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-21 
Deposition Author(s): Niemann, H.H., Schmoldt, H.U., Wentzel, A., Kolmar, H., Heinz, D.W.

Revision History  

• Version 1.0: 2005-11-21
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Advisory, Data collection, Derived calculations, Experimental preparation
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary