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)

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
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wwPDB Validation 3D Report Full Report

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This is version 1.1 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
Modeled Residue Count: 535
Deposited Residue Count: 578
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-27

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.