6Z82 | pdb_00006z82

Thalictrum flavumn Norcoclaurine synthase point mutant in complex with a transition state analoge

PDB DOI: https://doi.org/10.2210/pdb6Z82/pdb

Classification: LYASE
Organism(s): Thalictrum flavum subsp. glaucum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-06-02 Released: 2020-12-02
Deposition Author(s): Roddan, R., Sula, A., Keep, N.H.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Birkbeck College

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.246 (Depositor), 0.260 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Single step syntheses of (1S)-aryl-tetrahydroisoquinolines by norcoclaurine synthases

Roddan, R., Sula, A., Mendez-Sanchez, D., Subrizi, F., Lichman, B.R., Broomfield, J., Richter, M., Andexer, J.N., Ward, J.M., Keep, N.H., Hailes, H.C.

(2020) Commun Chem

DOI: https://doi.org/10.1038/s42004-020-00416-8

Macromolecule Content

Total Structure Weight: 18.45 kDa
Atom Count: 1,265
Modeled Residue Count: 159
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-norcoclaurine synthase	A	165	Thalictrum flavum subsp. glaucum	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q67A25
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QBW (Subject of Investigation/LOI) Query on QBW Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-[2-[(phenylmethyl)amino]ethyl]benzene-1,2-diol C₁₅ H₁₇ N O₂ VFXBAOSXGMLCEF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.246 (Depositor), 0.260 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.66	α = 90
b = 62.66	β = 90
c = 72.645	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/N01877X/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R021643/1
Birkbeck College	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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.