6RP3 | pdb_00006rp3

Truncated Norcoclaurine synthase with reaction intermediate mimic

• PDB DOI: https://doi.org/10.2210/pdb6RP3/pdb

• Classification: LYASE
• Organism(s): Thalictrum flavum subsp. glaucum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-05-13 Released: 2019-10-09 
• Deposition Author(s): Keep, N.H., Roddan, R., Sula, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.244 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Acceptance and Kinetic Resolution of alpha-Methyl-Substituted Aldehydes by Norcoclaurine Synthases

Roddan, R., Gygli, G., Sula, A., Lichman, B.R., Pleiss, J., Ward, J.M., Keep, N.H., Hailes, H.C.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b02699

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.7 kDa 
• Atom Count: 1,340 
• Modeled Residue Count: 160 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-norcoclaurine synthase	A	165	Thalictrum flavum subsp. glaucum	Mutation(s): 0  EC: 4.2.1.78 (PDB Primary Data), 3.5.99.14 (UniProt)
UniProt
Find proteins for Q67A25 (Thalictrum flavum subsp. glaucum) Explore Q67A25  Go to UniProtKB:  Q67A25

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KCZ (Subject of Investigation/LOI)	B [auth A]	4-[2-[[(2~{R})-2-phenylpropyl]amino]ethyl]benzene-1,2-diol C17 H21 N O2 NXTJHSKVIAFFNX-ZDUSSCGKSA-N
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.244 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.256	α = 90
b = 62.256	β = 90
c = 73.579	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-09 
Deposition Author(s): Keep, N.H., Roddan, R., Sula, A.

Revision History  

• Version 1.0: 2019-10-09
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description