7YPD | pdb_00007ypd

Discovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering

PDB DOI: https://doi.org/10.2210/pdb7YPD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodotorula toruloides
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-03 Released: 2024-02-07
Deposition Author(s): Watanabe, Y., Asano, Y., Hibi, M.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free:
0.200 (Depositor), 0.200 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Discovery and characterization of a new carbonyl reductase from Rhodotorula toluroides reducing fluoroketones, and X-ray analysis of the variant by rational engineering

Watanabe, Y., Asano, Y., Hibi, M.

To be published.

Macromolecule Content

Total Structure Weight: 53.53 kDa
Atom Count: 4,258
Modeled Residue Count: 480
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonyl reductase	A [auth B], B [auth A]	256	Rhodotorula toruloides	Mutation(s): 0 Gene Names: RHTO0S_28e01354g
UniProt
Find proteins for A0A061BJP9 (Rhodotorula toruloides) Explore A0A061BJP9 Go to UniProtKB: A0A061BJP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A061BJP9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain E [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth A]	C [auth B], D [auth B], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.27 Å
R-Value Free: 0.200 (Depositor), 0.200 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.362	α = 90
b = 65.084	β = 99.834
c = 79.769	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	Japan	--

Revision History (Full details and data files)

Version 1.0: 2024-02-07
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, 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.