SAXSdb — 1d8i

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

MRNA TRIPHOSPHATASE CET1

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	SULFATE ION × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CET1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–311； UniProt 241–549 Author chain B； PDBConstruct 3–311； UniProt 241–549 Author chain C； PDBConstruct 3–311； UniProt 241–549

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	1d8i
Deposition date deposition_date	1999-10-24
Structure title title	X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.
Keywords keywords	;RNA TRIPHOSPHATASE, BETA SUBUNIT, POLYNUCLEOTIDE 5'-TRIPHOSPHATASE, MRNA PROCESSING, MRNA CAPPING, NUCLEAR PROTEIN BETA BARREL, CATALYTIC DOMAIN, DIMER, SULFATE COMPLEX, 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.

1d8i__assembly_1__model_1

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

Download this curve (.dat)

1d8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d8i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.25 Å
Rg (electron density)	27.58 Å
Total Rg	28.21 Å
Atom count	4610
Residues	576
Excluded volume	82011 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d8i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1d8i__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 (3)

Entity 1 Entity 1 polymer

Description description	MRNA TRIPHOSPHATASE CET1
Molecular weight formula_weight	35691.5 kDa
EC 编号 ec_number	3.1.3.33
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7329

HMYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	414

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1d8ia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.63 — CYTH-like phosphatases
Superfamily Superfamily superfamily	d.63.1 — CYTH-like phosphatases
Family Family family	d.63.1.1 — mRNA triphosphatase CET1

Domain ID domain_id	d1d8ib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.63 — CYTH-like phosphatases
Superfamily Superfamily superfamily	d.63.1 — CYTH-like phosphatases
Family Family family	d.63.1.1 — mRNA triphosphatase CET1

Domain ID domain_id	d1d8ic_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.63 — CYTH-like phosphatases
Superfamily Superfamily superfamily	d.63.1 — CYTH-like phosphatases
Family Family family	d.63.1.1 — mRNA triphosphatase CET1

CATH v4.4 (3 domains)

Domain ID domain_id	1d8iA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	10 — mRNA triphosphatase Cet1-like

Domain ID domain_id	1d8iB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	10 — mRNA triphosphatase Cet1-like

Domain ID domain_id	1d8iC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	10 — mRNA triphosphatase Cet1-like

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Unit-cell length a length_a	121.358 Å
Unit-cell length b length_b	116.095 Å
Unit-cell length c length_c	82.310 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.2026
R_free r_free	0.2696

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.

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

MRNA TRIPHOSPHATASE CET1

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

1d8i__assembly_1__model_1

1d8i__assembly_1__model_1 | I(q)

1d8i__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION.

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

MRNA TRIPHOSPHATASE CET1

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

1d8i__assembly_1__model_1

1d8i__assembly_1__model_1 | I(q)

1d8i__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)