6TA8 | pdb_00006ta8

Crystal structure of the epimerization domain from the third module of tyrocidine synthetase B, TycB3(E)

• PDB DOI: https://doi.org/10.2210/pdb6TA8/pdb
• Entry: 6TA8 supersedes: 5M6P

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Brevibacillus parabrevis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-10-29 Released: 2020-11-18 
• Deposition Author(s): Fage, C.D., Marahiel, M.A.
• Funding Organization(s): German Research Foundation, LOEWE Center for Synthetic Microbiology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases

Fage, C.D., Kosol, S., Jenner, M., Oster, C., Gallo, A., Kaniusaite, M., Steinbach, R., Staniforth, M., Stavros, V.G., Marahiel, M.A., Cryle, M.J., Lewandowski, J.R.

(2021) ACS Catal 11: 10802-10813

• DOI: https://doi.org/10.1021/acscatal.1c02113

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 113.72 kDa 
• Atom Count: 7,424 
• Modelled Residue Count: 887 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrocidine synthase 2	A, B	496	Brevibacillus parabrevis	Mutation(s): 0  Gene Names: tycB EC: 5.1.1.11
UniProt
Find proteins for O30408 (Brevibacillus parabrevis) Explore O30408  Go to UniProtKB:  O30408

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.661	α = 90
b = 120.661	β = 90
c = 256.002	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
XDS	data reduction
Aimless	data scaling
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Fage, C.D., Marahiel, M.A.
• This entry supersedes: 5M6P

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--
LOEWE Center for Synthetic Microbiology	Germany	--

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-06-02
  Changes: Advisory
• Version 1.2: 2021-08-18
  Changes: Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-27
  Changes: Database references, Structure summary