SAXSdb — 4wjs

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

Rsa4

Chaetomium thermophilum

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 monomer Monomer Protein × 1 PDB declaration: Monomeric（1） Consistent with protein copy count	Chain A； UniProt 248–726	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2 mM KF, 20% PEG 3350	Resolution 1.80 Å R-free 0.211

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 4WJS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6QTA Crystal structure of Rea1-MIDAS/Rsa4-UBL complex from Chaetomium thermophilum Deposited 2019-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 30–128（99 aa）	Not recorded	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；2 M (NH4)2SO4, 5% PEG 400 and 0.1 M MES at pH 6.5	Resolution 1.89 Å R-free 0.211
8PV1 Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure Deposited 2023-07-17	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: 59-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.56 Å
8PV2 Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 Deposited 2023-07-17	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 × 54 PDB declaration: 57-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
8PV3 Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite structure Deposited 2023-07-17	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: 59-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8PV4 Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure Deposited 2023-07-17	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 × 62 PDB declaration: 66-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8PV5 Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite structure Deposited 2023-07-17	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 × 50 PDB declaration: 53-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
8PV6 Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure Deposited 2023-07-17	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 × 60 PDB declaration: 64-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8PV7 Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure Deposited 2023-07-17	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: 59-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.12 Å
8PV8 Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure Deposited 2023-07-17	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: 60-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
8PVK Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite structure Deposited 2023-07-17	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 × 56 PDB declaration: 60-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
8PVL Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure Deposited 2023-07-17	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 × 54 PDB declaration: 58-meric	Chain Ch 1–517（517 aa）	Mutation：E117D	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.19 Å

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

View Construct and Data Evidence

UniProt name	G0SC29_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–485； UniProt 248–726

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	4wjs
Deposition date deposition_date	2014-10-01
Structure title title	Crystal structure of Rsa4 from Chaetomium thermophilum
Keywords keywords	ribosome assembly, ribosome biogenesis, biosynthetic protein; BIOSYNTHETIC PROTEIN
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	23.93 Å
Radius of gyration Rg (electron density) rg_electron	23.22 Å
Forward intensity I(0) i0	49899200.00
Molecular weight molecular_weight	53907.0 kDa
Excluded volume excluded_volume	66952 Å³
Envelope volume envelope_volume	78529 Å³
Hydration-shell volume shell_volume	28276 Å³
Envelope diameter envelope_diameter	83.1 Å
Shell Rg shell_rg	30.31 Å
Envelope Rg envelope_rg	23.36 Å
Shape Rg shape_rg	23.20 Å
Total Rg total_rg	24.03 Å
Total atoms total_atoms	3809
Residues n_residues	485
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	81.3 Å
Rg (real space) rg_real	23.89 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	4.9900e+07
I(0) uncertainty (real space) i0_real_error	7.8980e+05
Rg (reciprocal space) rg_reciprocal	23.90 Å
I(0) (reciprocal space) i0_reciprocal	49900000.0000
Solution quality estimate total_estimate	0.7838
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	73.7 Å
Skewness Skewness skewness	0.391
Kurtosis Kurtosis kurtosis	-0.082
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11500000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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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	Rsa4
Molecular weight formula_weight	53999.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4269

DLGSFKANFIDSDGNQMTDVVEINFADATEKNISNLLNTLLGRDREEFTPYRFRIHIPGKDLIIDQYPNDLLSLLQKHGVTNPFETTITLSAEPQAIFKVHAVSRLAHRIPGHGQPILSCQFSPVSSSRLATGSGDNTARIWDTDSGTPKFTLKGHTGWVLGVSWSPDGKYLATCSMDTTVRVWDPESGKQVNQEFRGHAKWVLALAWQPYHLWRDGTARLASASKDCTVRIWLVNTGRTEHVLSGHKGSVSCVKWGGTDLIYTGSHDRSVRVWDAVKGTLVHNFTAHGHWVNHIALSSDHVLRTAYHDHTKEVPGTEEERRAKAKERFEKAAKIKGKVAERLVSASDDFTMYLWDPTNNGSKPVARLLGHQNKVNHVQFSPDGTLIASAGWDNSTKLWNARDGKFIKNLRGHVAPVYQCAWSADSRLVVTGSKDCTLKVWNVRTGKLAMDLPGHEDEVYAVDWAADGELVASGGKDKAVRTWRN

来源 Source

来源生物 organism	Chaetomium thermophilum
NCBI Class编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	445

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4wjsA01
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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8. Citations (1)

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Unit-cell length a length_a	48.155 Å
Unit-cell length b length_b	48.832 Å
Unit-cell length c length_c	58.625 Å
Unit-cell angle α angle_alpha	67.47 °
Unit-cell angle β angle_beta	88.39 °
Unit-cell angle γ angle_gamma	62.65 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	42.070 Å
R factor r_factor	0.1676
R_work r_work	0.1652
R_free r_free	0.2110

fit	/app/data/saxs_computation/wj/4wjs/4wjs.fit
pddf	/app/data/pr_computation/wj/4wjs/4wjs.pr.out
profile	/app/data/saxs_computation/wj/4wjs/4wjs.dat

Crystal structure of Rsa4 from Chaetomium thermophilum

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

Rsa4

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