7E2V

Crystal structure of MaDA-3

• PDB DOI: https://doi.org/10.2210/pdb7E2V/pdb

• Classification: PLANT PROTEIN
• Organism(s): Morus alba
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2021-02-07 Released: 2021-12-01 
• Deposition Author(s): Gao, L., Du, X., Fan, J., Lei, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Starting Model: experimental

Literature

Enzymatic control of endo- and exo-stereoselective Diels-Alder reactions with broad substrate scope.

Gao, L., Zou, Y., Liu, X., Yang, J., Du, X., Wang, J., Yu, X., Fan, J., Jiang, M., Li, Y., Houk, K.N., Lei, X.

(2021) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-021-00717-8

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 126.79 kDa 
• Atom Count: 7,885 
• Modelled Residue Count: 977 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MaDA-3	A, B	550	Morus alba	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.028	α = 90
b = 79.167	β = 98.232
c = 95.011	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-01 
Deposition Author(s): Gao, L., Du, X., Fan, J., Lei, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21625201

Revision History  

• Version 1.0: 2021-12-01
  Type: Initial release
  
• Version 1.1: 2021-12-22
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary