7W0K | pdb_00007w0k

plant glycosyltransferase

• PDB DOI: https://doi.org/10.2210/pdb7W0K/pdb

• Classification: TRANSFERASE
• Organism(s): Calotropis gigantea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-11-18 Released: 2022-03-02 
• Deposition Author(s): Wei, H., Feng, L.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Functional and Structural Dissection of a Plant Steroid 3-O-Glycosyltransferase Facilitated the Engineering Enhancement of Sugar Donor Promiscuity

Huang, W., He, Y., Jiang, R., Deng, Z., Long, F.

(2022) ACS Catal : 2927-2937

• DOI: https://doi.org/10.1021/acscatal.1c05729

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 54.63 kDa 
• Atom Count: 3,629 
• Modeled Residue Count: 457 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	480	Calotropis gigantea	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for A0A385Z7H9 (Calotropis gigantea) Explore A0A385Z7H9  Go to UniProtKB:  A0A385Z7H9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	B [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.462	α = 90
b = 74.038	β = 114.4
c = 61.815	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Wei, H., Feng, L.

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Funding Organization	Location	Grant Number
Other government		2018YFA0900400
Other government		2021YFA0909500
Other government	China	2042019kf0185

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description