SAXSdb — 3ko6

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1. Protein Identity and Related Structures Protein Identity & Related Structures

UPF0067 GAF domain-containing protein YKL069W

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	METHIONINE SULFOXIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YKG9_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 1–180 Author chain B； PDBConstruct 1–180； UniProt 1–180

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ko6
Deposition date deposition_date	2009-11-13
Structure title title	Crystal structure of yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate
Keywords keywords	;Saccharomyces cerevisiae, methionine-R-sulfoxide reductase, substrate binding, catalytic mechanism, product dissociation, OXIDOREDUCTASE ;; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3ko6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ko6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ko6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.48 Å
Rg (electron density)	19.30 Å
Total Rg	20.29 Å
Atom count	2738
Residues	352
Excluded volume	48657 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ko6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	UPF0067 GAF domain-containing protein YKL069W
Molecular weight formula_weight	19753.3 kDa
EC 编号 ec_number	1.8.4.14
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2854

MGSSTGFHHADHVNYSSNLNKEEILEQLLLSYEGLSDGQVNWVCNLSNASSLIWHAYKSLAVDINWAGFYVTQASEENTLILGPFQGKVACQMIQFGKGVCGTAASTKETQIVPDVNKYPGHIACDGETKSEIVVPIISNDGKTLGVIDIDCLDYEGFDHVDKEFLEKLAKLINKSCVFK

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	METHIONINE SULFOXIDE
Molecular weight formula_weight	165.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ko6a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.2 — GAF domain-like
Family Family family	d.110.2.1 — GAF domain

Domain ID domain_id	d3ko6b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.2 — GAF domain-like
Family Family family	d.110.2.1 — GAF domain

CATH v4.4 (2 domains)

Domain ID domain_id	3ko6A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

Domain ID domain_id	3ko6B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

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Unit-cell length a length_a	73.548 Å
Unit-cell length b length_b	73.548 Å
Unit-cell length c length_c	163.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	49.561 Å
R factor r_factor	0.2104
R_work r_work	0.2082
R_free r_free	0.2541

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

UPF0067 GAF domain-containing protein YKL069W

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ko6__assembly_1__model_1

3ko6__assembly_1__model_1 | I(q)

3ko6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

UPF0067 GAF domain-containing protein YKL069W

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ko6__assembly_1__model_1

3ko6__assembly_1__model_1 | I(q)

3ko6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)