8HO2 | pdb_00008ho2

crystal structure of Norcoclaurine synthase from Chinese lotus (Nelumbo nucicera)

PDB DOI: https://doi.org/10.2210/pdb8HO2/pdb

Classification: PLANT PROTEIN
Organism(s): Nelumbo nucifera
Expression System: Eschenbachia
Mutation(s): No

Deposited: 2022-12-09 Released: 2023-12-06
Deposition Author(s): Liao, L.J., Zhao, Y.C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.179 (Depositor), 0.179 (DCC)
R-Value Work:
0.157 (Depositor), 0.157 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
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Literature

Discovery, Structure, and Mechanism of the (R, S)-Norcoclaurine Synthase for the Chiral Synthesis of Benzylisoquinoline Alkaloids

Zhang, L., Zhang, S., Liao, L., Tang, H., Wang, W., Yin, F., Han, L., Zhu, K., Liu, Y., Xu, D., Wang, X., Qin, M., Xiao, Y., Sheng, X., Zhao, Y.

(2023) ACS Catal 13: 15164-15174

DOI: https://doi.org/10.1021/acscatal.3c03296

Macromolecule Content

Total Structure Weight: 36.9 kDa
Atom Count: 2,846
Modeled Residue Count: 313
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-norcoclaurine synthase	A, B	162	Nelumbo nucifera	Mutation(s): 0 Gene Names: LOC104590414, HUJ06_019302 EC: 4.2.1.78
UniProt
Find proteins for A0A191T7N6 (Nelumbo nucifera) Explore A0A191T7N6 Go to UniProtKB: A0A191T7N6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A191T7N6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.179 (Depositor), 0.179 (DCC)
R-Value Work: 0.157 (Depositor), 0.157 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.262	α = 90
b = 58.104	β = 90
c = 114.139	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81703637
National Natural Science Foundation of China (NSFC)	China	31970596

Revision History (Full details and data files)

Version 1.0: 2023-12-06
Type: Initial release
Version 1.1: 2024-12-18
Changes: Database references, 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.