6KFM | pdb_00006kfm

Amino-transferase (AMT) Domain of Hybrid Polyketide/Non-Ribosomal Peptide Synthetase

• PDB DOI: https://doi.org/10.2210/pdb6KFM/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-07-08 Released: 2019-09-25 
• Deposition Author(s): Tian, Q.W., Jiang, T.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure Insights into the Molecular Mechanism of Two Tailoring Domains of Hybrid Polyketide/Non-Ribosomal Peptide Synthetase

Tian, Q.W., Jiang, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 103.59 kDa 
• Atom Count: 7,828 
• Modeled Residue Count: 898 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycosubtilin synthase subunit A	A, B	461	Bacillus subtilis	Mutation(s): 0  Gene Names: mycA EC: 2.3.1
UniProt
Find proteins for Q9R9J1 (Bacillus subtilis) Explore Q9R9J1  Go to UniProtKB:  Q9R9J1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	E [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.534	α = 90
b = 89.492	β = 90
c = 136.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Tian, Q.W., Jiang, T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570768

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description