3KO6 | pdb_00003ko6

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 (Depositor), 0.245 (DCC)
R-Value Work:
0.208 (Depositor), 0.203 (DCC)
R-Value Observed:
0.210 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 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
Modeled Residue Count: 352
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 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]	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 (Depositor), 0.245 (DCC)
R-Value Work: 0.208 (Depositor), 0.203 (DCC)
R-Value Observed: 0.210 (Depositor)

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

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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
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, 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.