SAXSdb — 3oi7

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

Uncharacterized protein YKR043C

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	1,7-di-O-phosphono-beta-D-altro-hept-2-ulofuranose × 2 MAGNESIUM ION × 2 SODIUM ION × 3 1,2-ETHANEDIOL × 4 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	1,7-di-O-phosphono-beta-D-altro-hept-2-ulofuranose × 2 MAGNESIUM ION × 2 SODIUM ION × 2 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YK23_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–292； UniProt 1–271 Author chain B； PDBConstruct 22–292； UniProt 1–271 Author chain C； PDBConstruct 22–292； UniProt 1–271 Author chain D； PDBConstruct 22–292； UniProt 1–271

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	3oi7
Deposition date deposition_date	2010-08-18
Structure title title	Structure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate
Keywords keywords	;beta-furanose, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, alpha-beta, sedoheptulose-1, 7-bisphosphatase, phosphatase, hydrolase ;; HYDROLASE
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.

3oi7__assembly_1__model_1

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

Download this curve (.dat)

3oi7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3oi7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.53 Å
Rg (electron density)	23.31 Å
Total Rg	24.25 Å
Atom count	4267
Residues	514
Excluded volume	75415 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3oi7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3oi7__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein YKR043C
Molecular weight formula_weight	33661.9 kDa
EC 编号 ec_number	3.1.3.11
Mutation mutation	H13A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8833

MGSSHHHHHHSSGRENLYFQGMPSLTPRCIIVRAGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPDNITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVVVDDDLREWEYGDYEGMLTREIIELRKSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFAHGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDAGGIGVLSYAHHNIDEPALELAGPFVSPPEEESQHGDV

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	1,7-di-O-phosphono-beta-D-altro-hept-2-ulofuranose
Molecular weight formula_weight	370.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	246

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3oi7A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	3oi7B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	3oi7C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

Domain ID domain_id	3oi7D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1240 — Phosphoglycerate mutase-like

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Unit-cell length a length_a	58.559 Å
Unit-cell length b length_b	74.945 Å
Unit-cell length c length_c	83.615 Å
Unit-cell angle α angle_alpha	90.04 °
Unit-cell angle β angle_beta	89.92 °
Unit-cell angle γ angle_gamma	77.22 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	27.500 Å
R factor r_factor	0.2301
R_work r_work	0.2284
R_free r_free	0.2600

Structure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate

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

Uncharacterized protein YKR043C

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

3oi7__assembly_1__model_1

3oi7__assembly_1__model_1 | I(q)

3oi7__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the structure of the H13A mutant of Ykr043C in complex with sedoheptulose-1,7-bisphosphate

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

Uncharacterized protein YKR043C

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

3oi7__assembly_1__model_1

3oi7__assembly_1__model_1 | I(q)

3oi7__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)