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), 0.170 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.170 (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

View Full Validation Report

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

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.