6NEG | pdb_00006neg

N191D, F205S mutant of scoulerine-9-O methyltransferase from Thalictrum flavum complexed with S-ADENOSYL-L-HOMOCYSTEINE

PDB DOI: https://doi.org/10.2210/pdb6NEG/pdb

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

Deposited: 2018-12-17 Released: 2019-12-18
Deposition Author(s): Valentic, T.R., Smolke, C.D., Payne, J.T.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.174 (Depositor), 0.170 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and functional characterization of the scoulerine 9-O methyltransferase from Thalictrum flavum.

Valentic, T.R., Smolke, C.S., Payne, J.T.

To be published.

Macromolecule Content

Total Structure Weight: 82.25 kDa
Atom Count: 5,736
Modeled Residue Count: 688
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-scoulerine 9-O-methyltransferase	A, B	375	Thalictrum flavum subsp. glaucum	Mutation(s): 2 EC: 2.1.1.117
UniProt
Find proteins for Q5C9L2 (Thalictrum flavum subsp. glaucum) Explore Q5C9L2 Go to UniProtKB: Q5C9L2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5C9L2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.174 (Depositor), 0.170 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.6	α = 90
b = 84.24	β = 96.23
c = 67.48	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	DP1AT007886-05

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.