5I10 | pdb_00005i10

Crystal structure of spinosyn rhamnosyl 4'-O-methyltransferase spnh mutant T242Q from Saccharopolyspora Spinosa

• PDB DOI: https://doi.org/10.2210/pdb5I10/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharopolyspora spinosa
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2016-02-05 Released: 2017-02-08 
• Deposition Author(s): Lin, Y.-C., Huang, S.-P., Huang, B.-L., Chen, Y.-H., Chen, Y.-J., Chiu, H.-T.
• Funding Organization(s): National Science Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spinosyn rhamnosyl 4'-O-methyltransferase spnh mutant T242Q from Saccharopolyspora Spinosa

Lin, Y.-C., Huang, S.-P., Huang, B.-L., Chen, Y.-H., Chen, Y.-J., Chiu, H.-T.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.13 kDa 
• Atom Count: 1,622 
• Modeled Residue Count: 192 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable O-methyltransferase	A	250	Saccharopolyspora spinosa	Mutation(s): 1  Gene Names: spnH
UniProt
Find proteins for Q9ALM9 (Saccharopolyspora spinosa) Explore Q9ALM9  Go to UniProtKB:  Q9ALM9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.776	α = 90
b = 54.776	β = 90
c = 306.532	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-08 
Deposition Author(s): Lin, Y.-C., Huang, S.-P., Huang, B.-L., Chen, Y.-H., Chen, Y.-J., Chiu, H.-T.

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Funding Organization	Location	Grant Number
National Science Council	Taiwan	NSC102-2113-M006-003-MY2

Revision History  

• Version 1.0: 2017-02-08
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description