6I73

Structure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine and protocatechuic aldehyde

PDB DOI: https://doi.org/10.2210/pdb6I73/pdb

Classification: TRANSFERASE
Organism(s): Fragaria x ananassa
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2018-11-15 Released: 2019-11-27
Deposition Author(s): Heldner, A., Schiefner, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.148
R-Value Work: 0.122
R-Value Observed: 0.122

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into enzymatic formation of the strawberry flavor compound 2,5-dimethyl-4-methoxy-3(2H)-furanone

Heldner, A., Schiefner, A.

To be published.

Macromolecule Content

Total Structure Weight: 80.92 kDa
Atom Count: 6,816
Modelled Residue Count: 706
Deposited Residue Count: 724
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methyltransferase	A, B	362	Fragaria x ananassa	Mutation(s): 0 Gene Names: omt1 EC: 2.1.1.68
UniProt
Find proteins for Q9M602 (Fragaria ananassa) Explore Q9M602 Go to UniProtKB: Q9M602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9M602
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
H6N (Subject of Investigation/LOI) Query on H6N Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	Protocatechuic aldehyde C₇ H₆ O₃ IBGBGRVKPALMCQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth A], F [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.148
R-Value Work: 0.122
R-Value Observed: 0.122
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.376	α = 90
b = 87.655	β = 90
c = 146.814	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Heldner, A.

Schiefner, A.

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Data collection, Structure summary

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Help and Resources

6I73

Structure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine and protocatechuic aldehyde

Structural insights into enzymatic formation of the strawberry flavor compound 2,5-dimethyl-4-methoxy-3(2H)-furanone

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)