7ZB0 | pdb_00007zb0

macrocyclase OphP with 15mer

• PDB DOI: https://doi.org/10.2210/pdb7ZB0/pdb

• Classification: HYDROLASE
• Organism(s): Omphalotus olearius
• Expression System: Komagataella pastoris, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-03-23 Released: 2022-07-06 
• Deposition Author(s): Song, H., Naismith, J.H.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for the enzymatic macrocyclization of multiply backbone N-methylated peptides

Matabaro, E., Song, H., Gherlone, F., Sonderegger, L., Giltrap, A., Liver, S., Gossert, A., Kunzler, M., Naismith, J.H.

(2022) bioRxiv 

• DOI: https://doi.org/10.1101/2022.07.21.500988

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 345.01 kDa 
• Atom Count: 23,277 
• Modeled Residue Count: 2,891 
• Deposited Residue Count: 3,040 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prolyl endopeptidase	A, B, C, D	745	Omphalotus olearius	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
15mer	E, F, G, H	15	Omphalotus olearius	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	M [auth C], Q [auth D]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	I [auth B], K [auth C], L [auth C], R [auth D], S [auth D], T [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT	J [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
NA	N [auth C], O [auth C], P [auth C], U [auth D], V [auth D], W [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IML	E, F, G, H	L-PEPTIDE LINKING	C7 H15 N O2		ILE
MVA	E, F, G, H	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	E, F, G, H	PEPTIDE LINKING	C3 H7 N O2		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.266 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.22	α = 113.04
b = 106.18	β = 101.67
c = 114.79	γ = 93.24

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Song, H., Naismith, J.H.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R018189/1

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-01-25
  Changes: Database references
• Version 1.2: 2024-02-07
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary