SAXSdb — 3kyh

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

mRNA-capping enzyme subunit beta

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 241–549 Chain B； UniProt 241–549	Fragment：Triphosphatase domain	mRNA-capping enzyme subunit alpha × 2 （Q01159）	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

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 3KYH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D8H X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS. Deposited 1999-10-24	Different construct Different oligomeric state 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） Chain B 241–549（309 aa）	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
1D8H X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS. Deposited 1999-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 241–549（309 aa）	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
1D8I X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH A SULFATE ION. Deposited 1999-10-24	Different construct Different mutation/modification Different oligomeric state 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 construct Different oligomeric state 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

2 other PDB entries and 4 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 2–310； UniProt 241–549 Author chain B； PDBConstruct 2–310； UniProt 241–549

mRNA-capping enzyme subunit alpha

Saccharomyces cerevisiae

UniProt Q01159

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–459 Chain D； UniProt 1–459	Not recorded	mRNA-capping enzyme subunit beta × 2 （O13297）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	MCE1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–461； UniProt 1–459 Author chain D； PDBConstruct 3–461； UniProt 1–459

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	3kyh
Deposition date deposition_date	2009-12-06
Structure title title	Saccharomyces cerevisiae Cet1-Ceg1 capping apparatus
Keywords keywords	;Capping, RNA, 5' modification, triphosphatase, guanylyltransferase, complex, Hydrolase, mRNA capping, mRNA processing, Nucleus, Phosphoprotein, GTP-binding, Nucleotide-binding, Nucleotidyltransferase, Transferase, PROTEIN BINDING ;; PROTEIN BINDING
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	45.71 Å
Radius of gyration Rg (electron density) rg_electron	45.77 Å
Forward intensity I(0) i0	327589000.00
Molecular weight molecular_weight	151810.0 kDa
Excluded volume excluded_volume	191350 Å³
Envelope volume envelope_volume	285180 Å³
Hydration-shell volume shell_volume	53537 Å³
Envelope diameter envelope_diameter	154.7 Å
Shell Rg shell_rg	48.31 Å
Envelope Rg envelope_rg	44.80 Å
Shape Rg shape_rg	45.75 Å
Total Rg total_rg	45.96 Å
Total atoms total_atoms	10696
Residues n_residues	1326
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	149.7 Å
Rg (real space) rg_real	45.95 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	3.2760e+08
I(0) uncertainty (real space) i0_real_error	5.9420e+06
Rg (reciprocal space) rg_reciprocal	45.72 Å
I(0) (reciprocal space) i0_reciprocal	327500000.0000
Solution quality estimate total_estimate	0.8524
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.0 Å
Skewness Skewness skewness	0.378
Kurtosis Kurtosis kurtosis	-0.539
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27750000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.409

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	mRNA-capping enzyme subunit beta
Molecular weight formula_weight	35525.3 kDa
EC 编号 ec_number	3.1.3.33
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	10696

MYKNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	mRNA-capping enzyme subunit alpha
Molecular weight formula_weight	53030.3 kDa
EC 编号 ec_number	2.7.7.50
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SLMVLAMESRVAPEIPGLIQPGNVTQDLKMMVCKLLNSPKPTKTFPGSQPVSFQHSDVEEKLLAHDYYVCEKTDGLRVLMFIVINPVTGEQGCFMIDRENNYYLVNGFRFPRLPQKKKEELLETLQDGTLLDGELVIQTNPMTKLQELRYLMFDCLAINGRCLTQSPTSSRLAHLGKEFFKPYFDLRAAYPNRCTTFPFKISMKHMDFSYQLVKVAKSLDKLPHLSDGLIFTPVKAPYTAGGKDSLLLKWKPEQENTVDFKLILDIPMVEDPSLPKDDRNRWYYNYDVKPVFSLYVWQGGADVNSRLKHFDQPFDRKEFEILERTYRKFAELSVSDEEWQNLKNLEQPLNGRIVECAKNQETGAWEMLRFRDDKLNGNHTSVVQKVLESINDSVSLEDLEEIVGDIKRCWDERRANMAGGSGRPLPSQSQNATLSTSKPVHSQPPSNDKEPKYVDEDDWSD

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3kyha_
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	d3kyhb_
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 (6 domains)

Domain ID domain_id	3kyhA01
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	3kyhB01
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	3kyhC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	3kyhC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3kyhD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	3kyhD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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8. Citations (1)

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Unit-cell length a length_a	165.993 Å
Unit-cell length b length_b	165.993 Å
Unit-cell length c length_c	172.355 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.980 Å
R factor r_factor	0.2516
R_work r_work	0.2492
R_free r_free	0.2980

fit	/app/data/saxs_computation/ky/3kyh/3kyh.fit
pddf	/app/data/pr_computation/ky/3kyh/3kyh.pr.out
profile	/app/data/saxs_computation/ky/3kyh/3kyh.dat

Saccharomyces cerevisiae Cet1-Ceg1 capping apparatus

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

mRNA-capping enzyme subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

mRNA-capping enzyme subunit alpha

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)