7MSY

Structure of CalU17 from the Calicheamicin Biosynthesis Pathway of Micromonospora echinospora

PDB DOI: https://doi.org/10.2210/pdb7MSY/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Micromonospora echinospora
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-05-12 Released: 2021-07-28
Deposition Author(s): Kosgei, A.J., Miller, M.D., Xu, W., Van Lanen, S.G., Thorson, J.S., Phillips Jr., G.N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.236
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina.

Kosgei, A.J., Miller, M.D., Bhardwaj, M., Xu, W., Thorson, J.S., Van Lanen, S.G., Phillips Jr., G.N.

(2022) Acta Crystallogr F Struct Biol Commun 78: 1-7

PubMed: 34981769 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X21012322
Primary Citation of Related Structures:
6UBL, 7ML6, 7MSY

PubMed Abstract:
Dynemicin is an enediyne natural product from Micromonospora chersina ATCC53710. Access to the biosynthetic gene cluster of dynemicin has enabled the in vitro study of gene products within the cluster to decipher their roles in assembling this unique molecule. This paper reports the crystal structure of DynF, the gene product of one of the genes within the biosynthetic gene cluster of dynemicin. DynF is revealed to be a dimeric eight-stranded β-barrel structure with palmitic acid bound within a cavity. The presence of palmitic acid suggests that DynF may be involved in binding the precursor polyene heptaene, which is central to the synthesis of the ten-membered ring of the enediyne core.

Organizational Affiliation

Department of Biosciences, Rice University, Houston, TX 77251, USA.

Macromolecule Content

Total Structure Weight: 35.98 kDa
Atom Count: 2,580
Modelled Residue Count: 292
Deposited Residue Count: 317
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalU17	A	317	Micromonospora echinospora	Mutation(s): 0 Gene Names: calU17
UniProt
Find proteins for Q8KND1 (Micromonospora echinospora) Explore Q8KND1 Go to UniProtKB: Q8KND1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KND1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A]	J [auth A], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.236
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.465	α = 90
b = 53.465	β = 90
c = 223.468	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
XSCALE	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-07-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM115261
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01-CA217255
National Science Foundation (NSF, United States)	United States	STC-1231306