SAXSdb — 5jbm

▼

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

Chromatin assembly factor 1 subunit p90

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 457–606	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.3；291 K；0.2 M sodium formate, 14% PEG 3350, 0.1 M Tris, pH 8.3	Resolution 3.00 Å R-free 0.275

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 5JBM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5EJO Crystal structure of the winged helix domain in Chromatin assembly factor 1 subunit p90 Deposited 2015-11-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 519–606（88 aa） Fragment：UNP residues 519-606	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M NaCl, 1.5 M (NH4)2SO4, 0.1 M BIS-Tris	Resolution 2.75 Å R-free 0.230
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 136–225（90 aa） Fragment：KER domain, residues 136-225	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 136–225（90 aa） Fragment：KER domain, residues 136-225	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 136–225（90 aa） Fragment：KER domain, residues 136-225	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8DEI Structure of the Cac1 KER domain Deposited 2022-06-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 136–225（90 aa） Fragment：KER domain, residues 136-225	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；288 K；0.1 M Phosphate/citrate pH 4.2 and 30 % PEG 300	Resolution 2.81 Å R-free 0.282
8THW Cac1 PIP motif bound to PCNA Deposited 2023-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 222–240（19 aa） Chain B 222–240（19 aa） Chain C 222–240（19 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M magnesium acetate tetrahydrate (Mg Ac4H) and 11% w/v PEG3350	Resolution 2.60 Å R-free 0.267

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RLF2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–150； UniProt 457–606

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	5jbm
Deposition date deposition_date	2016-04-13
Structure title title	Crystal structgure of Cac1 C-terminus
Keywords keywords	nucleosome assembly, histone chaperone, CAF-1, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	13.99 Å
Radius of gyration Rg (electron density) rg_electron	12.56 Å
Forward intensity I(0) i0	1801800.00
Molecular weight molecular_weight	9122.0 kDa
Excluded volume excluded_volume	11442 Å³
Envelope volume envelope_volume	12766 Å³
Hydration-shell volume shell_volume	9145 Å³
Envelope diameter envelope_diameter	44.6 Å
Shell Rg shell_rg	17.71 Å
Envelope Rg envelope_rg	12.93 Å
Shape Rg shape_rg	12.53 Å
Total Rg total_rg	13.87 Å
Total atoms total_atoms	642
Residues n_residues	81
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	45.5 Å
Rg (real space) rg_real	13.94 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.8020e+06
I(0) uncertainty (real space) i0_real_error	2.2850e+04
Rg (reciprocal space) rg_reciprocal	13.94 Å
I(0) (reciprocal space) i0_reciprocal	1802000.0000
Solution quality estimate total_estimate	0.8885
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.1 Å
Skewness Skewness skewness	0.206
Kurtosis Kurtosis kurtosis	-0.315
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	214200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.973

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	58.850 Å
Unit-cell length b length_b	58.850 Å
Unit-cell length c length_c	97.929 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	29.425 Å
R factor r_factor	0.2374
R_work r_work	0.2331
R_free r_free	0.2749

Description description	Chromatin assembly factor 1 subunit p90
Molecular weight formula_weight	16962.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	654

Crystal structgure of Cac1 C-terminus

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

Chromatin assembly factor 1 subunit p90

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 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

fit	/app/data/saxs_computation/jb/5jbm/5jbm.fit
pddf	/app/data/pr_computation/jb/5jbm/5jbm.pr.out
profile	/app/data/saxs_computation/jb/5jbm/5jbm.dat