6I70 | pdb_00006i70

Structure of Fragaria ananassa O-methyltransferase - apo form

PDB DOI: https://doi.org/10.2210/pdb6I70/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: 2.10 Å
R-Value Free:
0.226 (Depositor), 0.219 (DCC)
R-Value Work:
0.202 (Depositor)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6I70

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: 79.56 kDa
Atom Count: 5,573
Modeled Residue Count: 702
Deposited Residue Count: 724
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9M602
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-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: 2.10 Å
R-Value Free: 0.226 (Depositor), 0.219 (DCC)
R-Value Work: 0.202 (Depositor)
R-Value Observed: 0.203 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.203	α = 90
b = 147.098	β = 90
c = 131.057	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):

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: 2024-11-13
Changes: 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.