6UHX | pdb_00006uhx

Crystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb6UHX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-29 Released: 2020-08-05
Deposition Author(s): Stogios, P.J., Skarina, T., Chen, C., Kagan, O., Iakounine, A., Savchenko, A.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.315 (Depositor), 0.320 (DCC)
R-Value Work:
0.235 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (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

Crystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae

Chen, C.

To be published.

Macromolecule Content

Total Structure Weight: 56.5 kDa
Atom Count: 4,058
Modeled Residue Count: 507
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase YIR035C	A, B	254	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: YIR035C EC: 1
UniProt
Find proteins for P40579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40579 Go to UniProtKB: P40579
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40579
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP 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]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-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: 2.75 Å
R-Value Free: 0.315 (Depositor), 0.320 (DCC)
R-Value Work: 0.235 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.545	α = 90
b = 73.049	β = 100.137
c = 67.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building
PHENIX	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	Industrial Biocatalysis Network

Revision History (Full details and data files)

Version 1.0: 2020-08-05
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.