SAXSdb — 7sfy

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

Protein Mis18-alpha

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 191–233 Chain B； UniProt 191–233	Not recorded	Protein Mis18-beta × 1 （O43482）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；Magnesium acetate, PEG 3350	Resolution 2.50 Å R-free 0.280
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 191–233 Chain E； UniProt 191–233	Not recorded	Protein Mis18-beta × 1 （O43482）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；Magnesium acetate, PEG 3350	Resolution 2.50 Å R-free 0.280

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 7SFY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SFZ Crystal structure of Mis18a-yippee domain Deposited 2021-10-04	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 77–190（114 aa） Chain B 77–190（114 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；Ammonium sulfate, PEG 400, HEPES	Resolution 3.00 Å R-free 0.250
7SFZ Crystal structure of Mis18a-yippee domain Deposited 2021-10-04	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 C 77–190（114 aa） Chain D 77–190（114 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；Ammonium sulfate, PEG 400, HEPES	Resolution 3.00 Å R-free 0.250
7SFZ Crystal structure of Mis18a-yippee domain Deposited 2021-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 77–190（114 aa） Chain F 77–190（114 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；Ammonium sulfate, PEG 400, HEPES	Resolution 3.00 Å R-free 0.250
7SFZ Crystal structure of Mis18a-yippee domain Deposited 2021-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 77–190（114 aa） Chain H 77–190（114 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；Ammonium sulfate, PEG 400, HEPES	Resolution 3.00 Å R-free 0.250
8S30 Crystal structure of human PLK1 Polo-Box Domain in complex with Mis18 Deposited 2024-02-19	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 B 49–55（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.09 M Halogen mix (NaF, NaBr, NaI), 0.1 M buffer system 2 (Sodium HEPES and MOPS) (pH7.5), 37% precipitant mix MPD_P1K_P3350 (MPD (racemic), PEG 1K, PEG 3350)	Resolution 1.94 Å R-free 0.271

2 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MS18A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–46； UniProt 191–233 Author chain B； PDBConstruct 4–46； UniProt 191–233 Author chain D； PDBConstruct 4–46； UniProt 191–233 Author chain E； PDBConstruct 4–46； UniProt 191–233

Protein Mis18-beta

Homo sapiens

UniProt O43482

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 188–229	Not recorded	Protein Mis18-alpha × 2 （Q9NYP9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；Magnesium acetate, PEG 3350	Resolution 2.50 Å R-free 0.280
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 188–229	Not recorded	Protein Mis18-alpha × 2 （Q9NYP9）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；Magnesium acetate, PEG 3350	Resolution 2.50 Å R-free 0.280

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	MS18B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–42； UniProt 188–229 Author chain F； PDBConstruct 1–42； UniProt 188–229

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	7sfy
Deposition date deposition_date	2021-10-04
Structure title title	Crystal structure of human Mis18ab_cc
Keywords keywords	Mis18ab complex, CELL CYCLE; CELL CYCLE
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	20.52 Å
Radius of gyration Rg (electron density) rg_electron	19.53 Å
Forward intensity I(0) i0	9097850.00
Molecular weight molecular_weight	23295.0 kDa
Excluded volume excluded_volume	29774 Å³
Envelope volume envelope_volume	36390 Å³
Hydration-shell volume shell_volume	16323 Å³
Envelope diameter envelope_diameter	69.1 Å
Shell Rg shell_rg	24.85 Å
Envelope Rg envelope_rg	19.83 Å
Shape Rg shape_rg	19.53 Å
Total Rg total_rg	20.42 Å
Total atoms total_atoms	1627
Residues n_residues	202
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	69.2 Å
Rg (real space) rg_real	20.49 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	9.0980e+06
I(0) uncertainty (real space) i0_real_error	1.2610e+05
Rg (reciprocal space) rg_reciprocal	20.49 Å
I(0) (reciprocal space) i0_reciprocal	9098000.0000
Solution quality estimate total_estimate	0.6562
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.235
Kurtosis Kurtosis kurtosis	-0.450
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3732000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 0.999; Sysdev: 0.387; Positv: 1.000; Valcen: 0.958; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein Mis18-alpha
Molecular weight formula_weight	5283.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	1643

SNAELFNLESRVEIEKSLTQMEDVLKALQMKLWEAESKLSFATCKS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein Mis18-beta
Molecular weight formula_weight	4807.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QNVPLSEKIAELKEKIVLTHNRLKSLMKILSEVTPDQSKPEN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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8. Citations (1)

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Unit-cell length a length_a	77.501 Å
Unit-cell length b length_b	101.815 Å
Unit-cell length c length_c	88.563 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	44.280 Å
R factor r_factor	0.2494
R_work r_work	0.2477
R_free r_free	0.2796

fit	/app/data/saxs_computation/sf/7sfy/7sfy.fit
pddf	/app/data/pr_computation/sf/7sfy/7sfy.pr.out
profile	/app/data/saxs_computation/sf/7sfy/7sfy.dat

Crystal structure of human Mis18ab_cc

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

Protein Mis18-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Protein Mis18-beta

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)