SAXSdb — 5wy3

▼

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

Putative uncharacterized protein

Chaetomium thermophilum var. thermophilum DSM 1495

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 472–872 Chain B； UniProt 472–872	Fragment：UNP residues 472-872	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Hepes-Na, 2.0 M ammonium sulfate	Resolution 3.20 Å R-free 0.266

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 5WY3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JPQ Cryo-EM structure of the 90S pre-ribosome Deposited 2016-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric	Chain G 1–1802（1802 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
5OQL Cryo-EM structure of the 90S pre-ribosome from Chaetomium thermophilum Deposited 2017-08-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric	Chain G 1–1802（1802 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
5WY4 Crystal structure of Chaetomium thermophilum Utp10 N-terminal domain Deposited 2017-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–471（471 aa） Fragment：N-terminal domain, UNP residues 1-471	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium citrate, 1.0 M ammonium dihydrogen phosphate	Resolution 2.50 Å R-free 0.264
5WYL Crystal structure of Chaetomium thermophilum Utp10 N-terminal domain in complex with Utp17 C-terminal helices Deposited 2017-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–471（471 aa） Fragment：N-terminal domain, UNP residues 1-471	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 20% w/v PEG 8000	Resolution 2.64 Å R-free 0.267
5WYL Crystal structure of Chaetomium thermophilum Utp10 N-terminal domain in complex with Utp17 C-terminal helices Deposited 2017-01-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–471（471 aa） Fragment：N-terminal domain, UNP residues 1-471	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 20% w/v PEG 8000	Resolution 2.64 Å R-free 0.267
6RXT Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state A Deposited 2019-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric	Chain UJ 1–1802（1802 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
6RXU Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B1 Deposited 2019-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 66-meric	Chain UJ 1–1802（1802 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
6RXV Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state B2 Deposited 2019-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain UJ 1–1802（1802 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6RXX Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state C, Poly-Ala Deposited 2019-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain UJ 1–1802（1802 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
6RXY Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state a Deposited 2019-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 59-meric	Chain UJ 1–1802（1802 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
6RXZ Cryo-EM structure of the 90S pre-ribosome (Kre33-Noc4) from Chaetomium thermophilum, state b Deposited 2019-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 68-meric	Chain UJ 1–1802（1802 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G0S5L1_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–401； UniProt 472–872 Author chain B； PDBConstruct 1–401； UniProt 472–872

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5wy3
Deposition date deposition_date	2017-01-10
Structure title title	Crystal structure of Chaetomium thermophilum Utp10 middle domain
Keywords keywords	nucleolar protein, components of 90S preribosome, RIBOSOMAL PROTEIN, NUCLEAR PROTEIN; RIBOSOMAL PROTEIN, NUCLEAR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	42.52 Å
Radius of gyration Rg (electron density) rg_electron	42.71 Å
Forward intensity I(0) i0	88916800.00
Molecular weight molecular_weight	80031.0 kDa
Excluded volume excluded_volume	101630 Å³
Envelope volume envelope_volume	141150 Å³
Hydration-shell volume shell_volume	29395 Å³
Envelope diameter envelope_diameter	147.2 Å
Shell Rg shell_rg	44.63 Å
Envelope Rg envelope_rg	41.35 Å
Shape Rg shape_rg	42.71 Å
Total Rg total_rg	42.84 Å
Total atoms total_atoms	5639
Residues n_residues	729
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

▼

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

Maximum dimension Dmax dmax	151.1 Å
Rg (real space) rg_real	43.04 Å
Rg uncertainty (real space) rg_real_error	2.00 Å
I(0) (real space) i0_real	8.8920e+07
I(0) uncertainty (real space) i0_real_error	1.7920e+06
Rg (reciprocal space) rg_reciprocal	42.53 Å
I(0) (reciprocal space) i0_reciprocal	88870000.0000
Solution quality estimate total_estimate	0.6784
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.5 Å
Skewness Skewness skewness	0.425
Kurtosis Kurtosis kurtosis	-0.808
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9065000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.245; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.175; Smooth: 0.906

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Unit-cell length a length_a	91.052 Å
Unit-cell length b length_b	91.052 Å
Unit-cell length c length_c	554.758 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	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	19.947 Å
R factor r_factor	0.2259
R_work r_work	0.2222
R_free r_free	0.2657

Description description	Putative uncharacterized protein
Molecular weight formula_weight	44242.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5639

Crystal structure of Chaetomium thermophilum Utp10 middle domain

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

Putative uncharacterized protein

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Chaetomium thermophilum var. thermophilum DSM 1495
NCBI Class编号 ncbi_taxonomy_id	759272
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/wy/5wy3/5wy3.fit
pddf	/app/data/pr_computation/wy/5wy3/5wy3.pr.out
profile	/app/data/saxs_computation/wy/5wy3/5wy3.dat