SAXSdb — 7sa9

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

Mucin-16

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 12665–12857	Fragment：SEA5 Domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；ammonium acetate, PEG 10000	Resolution 1.69 Å R-free 0.216
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 12665–12857	Fragment：SEA5 Domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；ammonium acetate, PEG 10000	Resolution 1.69 Å R-free 0.216

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 7SA9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8GKL Crystal Structure of the Humanized MUC16 Specific Antibody huAR9.6 Deposited 2023-03-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 12695–12821（127 aa） Fragment：SEA5 domain, residues 12695-12821	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M PCTP pH 4.0 25% PEG 1500	Resolution 2.60 Å R-free 0.269
8VM1 Structural Elucidation of the Mesothelin Mucin16 CA125 Interaction Deposited 2024-01-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 13475–13600（126 aa） Fragment：residues 296-359 of mesothelin (Uniprot numbering),SEA 10 domain of mucin-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Bis-Tris, NH4CL, PEG3350	Resolution 2.65 Å R-free 0.298
8VRS Mucin 16 peptide fused to MBP in complex with 4H11-scFv antibody Deposited 2024-01-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 14421–14446（26 aa） Fragment：residues 14421-14446 of mucin-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；0.1M Sodium Citrate, pH 5.0, 10mM Barium Chloride, 27% PEG MME 5000	Resolution 2.47 Å R-free 0.237
8VRS Mucin 16 peptide fused to MBP in complex with 4H11-scFv antibody Deposited 2024-01-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 14421–14446（26 aa） Fragment：residues 14421-14446 of mucin-16	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；0.1M Sodium Citrate, pH 5.0, 10mM Barium Chloride, 27% PEG MME 5000	Resolution 2.47 Å R-free 0.237

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MUC16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–196； UniProt 12665–12857 Author chain B； PDBConstruct 4–196； UniProt 12665–12857

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	7sa9
Deposition date deposition_date	2021-09-22
Structure title title	Human MUC16 SEA5 Domain
Keywords keywords	Mucin, CA125, ovarian cancer, pancreatic cancer, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	20.04 Å
Radius of gyration Rg (electron density) rg_electron	19.25 Å
Forward intensity I(0) i0	13369900.00
Molecular weight molecular_weight	27066.0 kDa
Excluded volume excluded_volume	33780 Å³
Envelope volume envelope_volume	40508 Å³
Hydration-shell volume shell_volume	18017 Å³
Envelope diameter envelope_diameter	67.7 Å
Shell Rg shell_rg	24.99 Å
Envelope Rg envelope_rg	19.47 Å
Shape Rg shape_rg	19.25 Å
Total Rg total_rg	20.09 Å
Total atoms total_atoms	3761
Residues n_residues	242
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	68.1 Å
Rg (real space) rg_real	20.02 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	1.3370e+07
I(0) uncertainty (real space) i0_real_error	1.7030e+05
Rg (reciprocal space) rg_reciprocal	20.02 Å
I(0) (reciprocal space) i0_reciprocal	13370000.0000
Solution quality estimate total_estimate	0.7004
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.357
Kurtosis Kurtosis kurtosis	-0.236
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2791000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 0.260; Positv: 1.000; Valcen: 0.993; Smooth: 0.979

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	78.540 Å
Unit-cell length b length_b	90.145 Å
Unit-cell length c length_c	42.821 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	58.360 Å
R factor r_factor	0.2009
R_work r_work	0.2000
R_free r_free	0.2160

Description description	Mucin-16
Molecular weight formula_weight	20717.2 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	4022

Human MUC16 SEA5 Domain

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

Mucin-16

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	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	204

fit	/app/data/saxs_computation/sa/7sa9/7sa9.fit
pddf	/app/data/pr_computation/sa/7sa9/7sa9.pr.out
profile	/app/data/saxs_computation/sa/7sa9/7sa9.dat