6UK5 | pdb_00006uk5

Structure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb6UK5/pdb

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


• Deposited: 2019-10-04 Released: 2020-10-07 
• Deposition Author(s): Alvarado, S.K., Miller, M.D., Xu, W., Wang, Z., 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 Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Structure of SAM bound CalS10, an amino pentose methyltransferase from Micromonospora echinaspora involved in calicheamicin biosynthesis

Alvarado, S.K., Miller, M.D., Xu, W., Wang, Z., Van Lanen, S.G., Thorson, J.S., Phillips Jr., G.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.87 kDa 
• Atom Count: 3,820 
• Modeled Residue Count: 476 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalS10	A, B	261	Micromonospora echinospora	Mutation(s): 0  Gene Names: calS10
UniProt
Find proteins for Q8KNF4 (Micromonospora echinospora) Explore Q8KNF4  Go to UniProtKB:  Q8KNF4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	D [auth A], H [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
1PE	F [auth A], J [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	C [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	E [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.29	α = 90
b = 133.29	β = 90
c = 81.76	γ = 120

Software Package:

Software Name	Purpose
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-07 
Deposition Author(s): Alvarado, S.K., Miller, M.D., Xu, W., Wang, Z., 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	R01GM115261
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM098248
National Science Foundation (NSF, United States)	United States	STC 1231306

Revision History  

• Version 1.0: 2020-10-07
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description