SAXSdb — 7sfz

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 77–190 Chain B； UniProt 77–190	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 77–190 Chain D； UniProt 77–190	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 77–190 Chain F； UniProt 77–190	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
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 77–190 Chain H； UniProt 77–190	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

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 7SFZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SFY Crystal structure of human Mis18ab_cc Deposited 2021-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 191–233（43 aa） Chain B 191–233（43 aa）	Not recorded	No recorded non-water small molecule	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
7SFY Crystal structure of human Mis18ab_cc Deposited 2021-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 191–233（43 aa） Chain E 191–233（43 aa）	Not recorded	No recorded non-water small molecule	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
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 ligand/ion 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 3 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 1–114； UniProt 77–190 Author chain B； PDBConstruct 1–114； UniProt 77–190 Author chain C； PDBConstruct 1–114； UniProt 77–190 Author chain D； PDBConstruct 1–114； UniProt 77–190 Author chain E； PDBConstruct 1–114； UniProt 77–190 Author chain F； PDBConstruct 1–114； UniProt 77–190 Author chain G； PDBConstruct 1–114； UniProt 77–190 Author chain H； PDBConstruct 1–114； UniProt 77–190

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	7sfz
Deposition date deposition_date	2021-10-04
Structure title title	Crystal structure of Mis18a-yippee domain
Keywords keywords	Mis18a, 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	34.36 Å
Radius of gyration Rg (electron density) rg_electron	34.14 Å
Forward intensity I(0) i0	121045000.00
Molecular weight molecular_weight	84004.0 kDa
Excluded volume excluded_volume	103560 Å³
Envelope volume envelope_volume	149040 Å³
Hydration-shell volume shell_volume	35982 Å³
Envelope diameter envelope_diameter	127.2 Å
Shell Rg shell_rg	41.38 Å
Envelope Rg envelope_rg	33.46 Å
Shape Rg shape_rg	34.24 Å
Total Rg total_rg	34.41 Å
Total atoms total_atoms	5780
Residues n_residues	748
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	113.5 Å
Rg (real space) rg_real	34.33 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	1.2100e+08
I(0) uncertainty (real space) i0_real_error	1.9410e+06
Rg (reciprocal space) rg_reciprocal	34.35 Å
I(0) (reciprocal space) i0_reciprocal	121000000.0000
Solution quality estimate total_estimate	0.8980
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.5 Å
Skewness Skewness skewness	0.231
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6658000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.916

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Protein Mis18-alpha
Molecular weight formula_weight	12795.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D,E,F,G,H
Atom count atom_count	5788

EERPLVFLCSGCRRPLGDSLSWVASQEDTNCILLRCVSCNVSVDKEQKLSKREKENGCVLETLCCAGCSLNLGYVYRCTPKNLDYKRDLFCLSVEAIESYVLGSSEKQIVSEDK

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	110.725 Å
Unit-cell length b length_b	114.864 Å
Unit-cell length c length_c	116.270 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.002 Å
Low-resolution limit resolution_low	49.985 Å
R factor r_factor	0.2058
R_work r_work	0.2026
R_free r_free	0.2500

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

Crystal structure of Mis18a-yippee domain

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

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