SAXSdb — 1d8h

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 241–549 Chain B； UniProt 241–549	Not recorded	MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.34；295 K；0.1M MES, 38% SATURATED (NH4)2SO4, 5MM DTT STABILIZED IN 2.5M AMSO4 + BUFFER, 200MM MNCL2 IN STABILIZATION CONDITION FOR MANGANESE COMPLEX, pH 6.34, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.310
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 241–549	Not recorded	MN MANGANESE (II) ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.34；295 K；0.1M MES, 38% SATURATED (NH4)2SO4, 5MM DTT STABILIZED IN 2.5M AMSO4 + BUFFER, 200MM MNCL2 IN STABILIZATION CONDITION FOR MANGANESE COMPLEX, pH 6.34, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.310

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1D8H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D8I X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION. Deposited 1999-10-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 241–549（309 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.34；295 K；0.1M MES, 38% SATURATED (NH4)2SO4, 5MM DTT STABILIZED IN 2.5M AMSO4 + BUFFER, pH 6.34, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.05 Å R-free 0.270
1D8I X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION. Deposited 1999-10-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 241–549（309 aa） Chain C 241–549（309 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.34；295 K；0.1M MES, 38% SATURATED (NH4)2SO4, 5MM DTT STABILIZED IN 2.5M AMSO4 + BUFFER, pH 6.34, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.05 Å R-free 0.270
3KYH Saccharomyces cerevisiae Cet1-Ceg1 capping apparatus Deposited 2009-12-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 241–549（309 aa） Fragment：Triphosphatase domain Chain B 241–549（309 aa） Fragment：Triphosphatase domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；1.0 M ammonium citrate, 0.1 M sodium citrate, 1.0% PEG (polyethylene glycerol) 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.298

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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	1d8h
Deposition date deposition_date	1999-10-24
Structure title title	X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.
Keywords keywords	;RNA TRIPHOSPHATASE, BETA SUBUNIT, POLYNUCLEOTIDE 5'-TRIPHOSPHATASE, mRNA PROCESSING, mRNA CAPPING, NUCLEAR PROTEIN BETA BARREL, CATALYTIC DOMAIN, DIMER, MANGANESE-SULFATE COMPLEX, HYDROLASE ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	36.89 Å
Radius of gyration Rg (electron density) rg_electron	37.07 Å
Forward intensity I(0) i0	147967000.00
Molecular weight molecular_weight	98806.0 kDa
Excluded volume excluded_volume	124210 Å³
Envelope volume envelope_volume	169450 Å³
Hydration-shell volume shell_volume	40524 Å³
Envelope diameter envelope_diameter	132.6 Å
Shell Rg shell_rg	40.28 Å
Envelope Rg envelope_rg	37.00 Å
Shape Rg shape_rg	37.08 Å
Total Rg total_rg	37.23 Å
Total atoms total_atoms	6957
Residues n_residues	864
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	126.5 Å
Rg (real space) rg_real	37.27 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	1.4800e+08
I(0) uncertainty (real space) i0_real_error	3.0700e+06
Rg (reciprocal space) rg_reciprocal	37.04 Å
I(0) (reciprocal space) i0_reciprocal	147900000.0000
Solution quality estimate total_estimate	0.8040
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.4 Å
Skewness Skewness skewness	0.544
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28630000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.692; Smooth: 0.732

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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	7626

HMYRNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	3

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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	669

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1d8ha_
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	d1d8hb_
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	d1d8hc_
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	1d8hA00
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	1d8hB00
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	1d8hC00
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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8. Citations (1)

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Unit-cell length a length_a	116.436 Å
Unit-cell length b length_b	118.723 Å
Unit-cell length c length_c	85.138 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.06 °
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	2.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.3100

fit	/app/data/saxs_computation/d8/1d8h/1d8h.fit
pddf	/app/data/pr_computation/d8/1d8h/1d8h.pr.out
profile	/app/data/saxs_computation/d8/1d8h/1d8h.dat

X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS.

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction