5EGF | pdb_00005egf

The crystal structure of SeMet-CT

• PDB DOI: https://doi.org/10.2210/pdb5EGF/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Penicillium aethiopicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-10-27 Released: 2016-10-19 
• Deposition Author(s): Zhang, J.R., Tang, Y., Zhou, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.266 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Structural basis of nonribosomal peptide macrocyclization in fungi

Zhang, J., Liu, N., Cacho, R.A., Gong, Z., Liu, Z., Qin, W., Tang, C., Tang, Y., Zhou, J.

(2016) Nat Chem Biol 12: 1001-1003

• PubMed: 27748753 
• DOI: https://doi.org/10.1038/nchembio.2202
• Primary Citation Related Structures: 
  5DIJ, 5DLK, 5EGF, 5EJD


• PubMed Abstract: 
  

  Nonribosomal peptide synthetases (NRPSs) in fungi biosynthesize important pharmaceutical compounds, including penicillin, cyclosporine and echinocandin. To understand the fungal strategy of forging the macrocyclic peptide linkage, we determined the crystal structures of the terminal condensation-like (C _T ) domain and the holo thiolation (T)-C _T complex of Penicillium aethiopicum TqaA. The first, to our knowledge, structural depiction of the terminal module in a fungal NRPS provides a molecular blueprint for generating new macrocyclic peptide natural products.

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Organizational Affiliation: 
• State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
Department of Pharmacology, Zhejiang University School of Medicine, Hangzhou, 430071, China.
National Center for Protein Science Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.
Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 30 Meilong Road, Shanghai 200237, China.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (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: 222.54 kDa 
• Atom Count: 14,879 
• Modeled Residue Count: 1,771 
• Deposited Residue Count: 1,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TqaA	A, B, C, D	486	Penicillium aethiopicum	Mutation(s): 2
UniProt
Find proteins for F1CWE4 (Penicillium aethiopicum) Explore F1CWE4  Go to UniProtKB:  F1CWE4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C8E	FA [auth C], L [auth A], QA [auth D], W [auth B]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C16 H34 O5 FEOZZFHAVXYAMB-UHFFFAOYSA-N
EDO	AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], LA [auth D], M [auth B], MA [auth D], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], PA [auth D], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.266 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 216.602	α = 90
b = 100.284	β = 100.18
c = 128.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
AutoSol	model building
HKL-2000	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Zhang, J.R., Tang, Y., Zhou, J.H.

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2016-11-30
  Changes: Database references
• Version 1.2: 2020-02-19
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Structure summary