3KO6

Crystal structure of yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate

PDB DOI: https://doi.org/10.2210/pdb3KO6/pdb

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

Deposited: 2009-11-13 Released: 2010-11-17
Deposition Author(s): Ma, X.-X., Guo, P.-C., Chen, Y., Zhou, C.-Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.254
R-Value Work: 0.208
R-Value Observed: 0.210

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 yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate

Ma, X.-X., Guo, P.-C., Chen, Y., Zhou, C.-Z.

To be published.

Macromolecule Content

Total Structure Weight: 39.84 kDa
Atom Count: 2,854
Modelled Residue Count: 352
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0067 GAF domain-containing protein YKL069W	A, B	180	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: YKL069W EC: 1.8.4.14
UniProt
Find proteins for P36088 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36088 Go to UniProtKB: P36088
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36088
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SME Query on SME 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]	C [auth A], D [auth B]	METHIONINE SULFOXIDE C₅ H₁₁ N O₃ S QEFRNWWLZKMPFJ-ZXPFJRLXSA-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: 2.55 Å
R-Value Free: 0.254
R-Value Work: 0.208
R-Value Observed: 0.210
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.548	α = 90
b = 73.548	β = 90
c = 163.56	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-11-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.