SAXSdb — 1nkq

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

Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region

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	CALCIUM ION × 2 SULFATE ION × 5 ACETIC ACID × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 SULFATE ION × 1 ACETIC ACID × 4 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 SULFATE ION × 1 ACETIC ACID × 4 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	CALCIUM ION × 6 SULFATE ION × 7 ACETIC ACID × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YNQ8_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–259； UniProt 1–259 Author chain B； PDBConstruct 1–259； UniProt 1–259 Author chain C； PDBConstruct 1–259； UniProt 1–259 Author chain D； PDBConstruct 1–259； UniProt 1–259 Author chain E； PDBConstruct 1–259； UniProt 1–259 Author chain F； PDBConstruct 1–259； UniProt 1–259

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	1nkq
Deposition date deposition_date	2003-01-03
Structure title title	Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein
Keywords keywords	;dimer, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, Structural Genomics, Unknown Function ;; Structural Genomics, Unknown Function
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.

1nkq__assembly_1__model_1

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

Download this curve (.dat)

1nkq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nkq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.50 Å
Rg (electron density)	22.20 Å
Total Rg	23.01 Å
Atom count	3848
Residues	481
Excluded volume	68776 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nkq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nkq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1nkq__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1nkq__assembly_4__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region
Molecular weight formula_weight	29111.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12088

MSYNYLKAARKIICIGRNYAAHIKELNNSTPKQPFFFLKPTSSIVTPLSSSLVKTTRPANSTFNGLNEDGTNPGPIFIPRGVKVHHEIELALIVSKHLSNVTKMKPEEVYDSISGVALALDLTARNVQDEAKKKGLPWTISKGFDTFMPISAIVSREKFSSYKSNLQDIFRVKCSVNGQLRQDGGTNLMLHPLHKILQHISTMISLEPGDIILTGTPAGVGELKPGDRVHCELLQNNDNIVDMNFECENRPGPYEFRET

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	634

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1nkqa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nkqb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nkqc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nkqd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nkqe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

Domain ID domain_id	d1nkqf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.177 — FAH
Superfamily Superfamily superfamily	d.177.1 — FAH
Family Family family	d.177.1.1 — FAH

CATH v4.4 (6 domains)

Domain ID domain_id	1nkqA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nkqB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nkqC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nkqD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nkqE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

Domain ID domain_id	1nkqF00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	850 — Fumarylacetoacetate hydrolase; domain 2
Homologous superfamily homologous superfamily	10 — Fumarylacetoacetase-like, C-terminal domain

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Unit-cell length a length_a	57.705 Å
Unit-cell length b length_b	85.990 Å
Unit-cell length c length_c	316.704 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2160
R_free r_free	0.2620

Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein

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

Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region

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

1nkq__assembly_1__model_1

1nkq__assembly_1__model_1 | I(q)

1nkq__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of yeast ynq8, a fumarylacetoacetate hydrolase family protein

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

Hypothetical 28.8 kDa protein in PSD1-SKO1 intergenic region

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

1nkq__assembly_1__model_1

1nkq__assembly_1__model_1 | I(q)

1nkq__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)