6V04

DynU16 crystal structure, a putative protein in the dynemicin biosynthetic locus

• PDB DOI: https://doi.org/10.2210/pdb6V04/pdb

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


• Deposited: 2019-11-18 Released: 2020-11-18 
• Deposition Author(s): Alvarado, S.K., Miller, M.D., Bhardwaj, M., Thorson, J.S., Van Lanen, S.G., 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: 1.50 Å
• R-Value Free: 0.188 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

Structural characterization of DynU16, a START/Bet v1-like protein involved in dynemicin biosynthesis.

Alvarado, S.K., Miller, M.D., Bhardwaj, M., Thorson, J.S., Van Lanen, S.G., Phillips Jr., G.N.

(2021) Acta Crystallogr F Struct Biol Commun 77: 328-333

• PubMed: 34605436 
• DOI: https://doi.org/10.1107/S2053230X21008943
• Primary Citation of Related Structures:  
  6V04


• PubMed Abstract: 
  

  The 1.5 Å resolution crystal structure of DynU16, a protein identified in the dynemicin-biosynthetic gene cluster, is reported. The structure adopts a di-domain helix-grip fold with a uniquely positioned open cavity connecting the domains. The elongated dimensions of the cavity appear to be compatible with the geometry of a linear polyene, suggesting the involvement of DynU16 in the upstream steps of dynemicin biosynthesis.

---

Organizational Affiliation: 

Department of BioSciences, Rice University, 6100 Main Street, Houston, TX 77005, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.09 kDa 
• Atom Count: 2,491 
• Modelled Residue Count: 269 
• Deposited Residue Count: 284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized SRPBCC domain-containing protein	A	284	Micromonospora chersina	Mutation(s): 0  Gene Names: GA0070603_4194
UniProt
Find proteins for B2BM46 (Micromonospora chersina) Explore B2BM46  Go to UniProtKB:  B2BM46

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.188 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.171	α = 90
b = 73.171	β = 90
c = 123.944	γ = 120

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
SHELX	phasing
HKL2Map	phasing
XDS	data scaling
XDS	data reduction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Alvarado, S.K., Miller, M.D., Bhardwaj, M., Thorson, J.S., Van Lanen, S.G., Phillips Jr., G.N.

---

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

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 2.0: 2021-04-28
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2021-09-15
  Changes: Database references, Structure summary
• Version 2.2: 2022-04-06
  Changes: Database references
• Version 2.3: 2024-05-22
  Changes: Data collection