4CDZ | pdb_00004cdz

Crystal Structure of Spinosyn Rhamnosyl 4'-O-Methyltransferase SpnH from Saccharopolyspora spinosa

• PDB DOI: https://doi.org/10.2210/pdb4CDZ/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharopolyspora spinosa
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-11-08 Released: 2014-11-26 
• 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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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure and Functional Insights of Spinosyn Rhamnosyl 4'-O-Methyltransferase Spnh from Saccharopolyspora Spinosa

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

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 29.18 kDa 
• Atom Count: 1,541 
• Modeled Residue Count: 193 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-METHYLTRANSFERASE	A	258	Saccharopolyspora spinosa	Mutation(s): 0
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: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.773	α = 90
b = 54.773	β = 90
c = 307.937	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Lin, Y.-C., Huang, S.-P., Huang, B.-L., Chen, Y.-H., Chen, Y.-J., Chiu, H.-T.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 2.0: 2023-12-20
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description