2C4B | pdb_00002c4b

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.164 (Depositor), 0.177 (DCC)
R-Value Work:
0.132 (Depositor), 0.146 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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 Biology 356: 1

PubMed: 16337652 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2005.11.005
Primary Citation 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.

Organizational Affiliation

Division of Structural Biology, German Research Centre for Biotechnology (GBF) Mascheroder Weg 1, D-38124 Braunschweig, Germany. hartmut.niemann@gbf.de

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 P00648 (Bacillus amyloliquefaciens) Explore P00648 Go to UniProtKB: P00648
Find proteins for P12071 (Ecballium elaterium) Explore P12071 Go to UniProtKB: P12071
Find proteins for P82409 (Momordica cochinchinensis) Explore P82409 Go to UniProtKB: P82409
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P82409 P00648 P12071
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain IA [auth B] SDF format, chain JA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B]	C [auth A], D [auth A], IA [auth B], JA [auth B]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain IA [auth B] Focus chain JA [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain IA [auth B] Focus chain JA [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] MOL2 format, chain KA [auth B] mmCIF format, chain KA [auth B]	KA [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Interactions & Density Focus chain KA [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B] mmCIF format, chain ZA [auth B]	HA [auth B] L [auth A] M [auth A] N [auth A] O [auth A] 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		Interactions Focus chain HA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain HA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] LA [auth B] 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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	AB [auth B], J [auth A], K [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain AB [auth B] Focus chain J [auth A] Focus chain K [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain W [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain W [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain W [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] 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		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.164 (Depositor), 0.177 (DCC)
R-Value Work: 0.132 (Depositor), 0.146 (DCC)
R-Value Observed: 0.133 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-11-21

Deposition Author(s):

Revision History (Full details and data files)

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