6VQP | pdb_00006vqp

Structure of CalU17 from the Calicheamicin Biosynthesis Pathway of Micromonospora echinospora

• PDB DOI: https://doi.org/10.2210/pdb6VQP/pdb

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


• Deposited: 2020-02-05 Released: 2021-02-17 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Structure of DynF from the Dynemicin Biosynthesis Pathway of Micromonospora chersina

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.52 kDa 
• Atom Count: 2,723 
• Modeled Residue Count: 300 
• Deposited Residue Count: 354 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalU17	A	335	Micromonospora echinospora	Mutation(s): 0  Gene Names: calU17
UniProt
Find proteins for Q8KND1 (Micromonospora echinospora) Explore Q8KND1  Go to UniProtKB:  Q8KND1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CalU17 His-Tagged protein	B [auth Q]	19	Micromonospora echinospora	Mutation(s): 0  Gene Names: calU17

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.951	α = 90
b = 53.951	β = 90
c = 218.923	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Kosgei, A.J., Miller, M.D., Xu, W., Van Lanen, S.G., Thorson, J.S., Phillips Jr., G.N.

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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: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description