7WZG | pdb_00007wzg

Cypemycin N-terminal methyltransferase CypM

• PDB DOI: https://doi.org/10.2210/pdb7WZG/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-18 Released: 2023-02-22 
• Deposition Author(s): Duan, S.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: in silico

Literature

Structural and mechanism analysis of cypm

Duan, S.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 174.65 kDa 
• Atom Count: 11,693 
• Modeled Residue Count: 1,428 
• Deposited Residue Count: 1,590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cypemycin N-terminal methyltransferase	A, B, C, D, E, F	265	Streptomyces sp.	Mutation(s): 0  Gene Names: cypM EC: 2.1.1.301
UniProt
Find proteins for E5KIC0 (Streptomyces sp) Explore E5KIC0  Go to UniProtKB:  E5KIC0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 245.111	α = 90
b = 245.111	β = 90
c = 81.653	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-22 
Deposition Author(s): Duan, S.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-22
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description