8ZC7

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): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.254
R-Value Work: 0.200
R-Value Observed: 0.204

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

Xia, M., Dong, D.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X5Q9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.66 Å
R-Value Free: 0.254
R-Value Work: 0.200
R-Value Observed: 0.204
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

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Entry History & Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-11-27
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.