8ZC7 | pdb_00008zc7

Crystallographic analysis of MitM, which catalyzes the post-mitosane modification in mitomycin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb8ZC7/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces caespitosus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-04-28 Released: 2024-11-27 
• Deposition Author(s): Xia, M., Dong, D.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: in silico

Literature

Crystallographic analysis of MitM, which catalyzes the post-mitosane modification in mitomycin biosynthesis

Xia, M., Dong, D.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 63.83 kDa 
• Atom Count: 4,142 
• Modeled Residue Count: 535 
• Deposited Residue Count: 578 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MitM	A, B	289	Streptomyces caespitosus	Mutation(s): 0  Gene Names: mitM
UniProt
Find proteins for Q9X5Q9 (Streptomyces lavendulae) Explore Q9X5Q9  Go to UniProtKB:  Q9X5Q9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.357	α = 90
b = 113.357	β = 90
c = 110.044	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
PDB_EXTRACT	data extraction
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Xia, M., Dong, D.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2303100

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Author supporting evidence