7E2V | pdb_00007e2v

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free:
0.308 (Depositor), 0.311 (DCC)
R-Value Work:
0.267 (Depositor), 0.268 (DCC)
R-Value Observed:
0.269 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.308 (Depositor), 0.311 (DCC)
R-Value Work: 0.267 (Depositor), 0.268 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-12-01

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.