8ZC8 | pdb_00008zc8

The structure of MitM and mitomycin A with SAH in mitomycin

PDB DOI: https://doi.org/10.2210/pdb8ZC8/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: 2.80 Å
R-Value Free:
0.244 (Depositor), 0.241 (DCC)
R-Value Work:
0.224 (Depositor), 0.226 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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: 63.29 kDa
Atom Count: 4,212
Modeled Residue Count: 552
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MitM	A, B	283	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
MQA (Subject of Investigation/LOI) Query on MQA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	[(1aS,8S,8aR,8bS)-6,8a-dimethoxy-5-methyl-4,7-dioxo-1,1a,2,4,7,8,8a,8b-octahydroazireno[2',3':3,4]pyrrolo[1,2-a]indol-8-yl]methyl carbamate C₁₆ H₁₉ N₃ O₆ HYFMSAFINFJTFH-NGSRAFSJSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.244 (Depositor), 0.241 (DCC)
R-Value Work: 0.224 (Depositor), 0.226 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.953	α = 90
b = 113.953	β = 90
c = 108.771	γ = 120

Software Package:

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

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.