SAXSdb — 6mfo

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

Protocadherin-15

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 27–396	Mutation：G16D N369D Q370N	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.7；277 K；0.1 M HEPES pH 7.7, 66% MPD, 4% Glycerol	Resolution 3.15 Å R-free 0.288

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 6MFO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6N2E Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N and Mouse Cadherin-23 EC1-2 T15E Deposited 2018-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–396（370 aa） Chain B 27–396（370 aa）	Mutation：G16D, N369D, Q370N Mutation：G16D, N369D, Q370N	CA CALCIUM ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Imidazole pH 6.8, 46% MPD	Resolution 2.90 Å R-free 0.253

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A087X1T6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–372； UniProt 27–396

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	6mfo
Deposition date deposition_date	2018-09-11
Structure title title	Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N
Keywords keywords	Mechanotransduction, Calcium-binding protein, stereocilia, hair cell, tip link, CELL ADHESION; CELL ADHESION
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	38.58 Å
Radius of gyration Rg (electron density) rg_electron	41.24 Å
Forward intensity I(0) i0	22802300.00
Molecular weight molecular_weight	37520.0 kDa
Excluded volume excluded_volume	46853 Å³
Envelope volume envelope_volume	65108 Å³
Hydration-shell volume shell_volume	17632 Å³
Envelope diameter envelope_diameter	151.2 Å
Shell Rg shell_rg	33.52 Å
Envelope Rg envelope_rg	41.69 Å
Shape Rg shape_rg	41.24 Å
Total Rg total_rg	40.66 Å
Total atoms total_atoms	2634
Residues n_residues	333
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	145.8 Å
Rg (real space) rg_real	39.96 Å
Rg uncertainty (real space) rg_real_error	2.62 Å
I(0) (real space) i0_real	2.2800e+07
I(0) uncertainty (real space) i0_real_error	4.7040e+05
Rg (reciprocal space) rg_reciprocal	39.11 Å
I(0) (reciprocal space) i0_reciprocal	22780000.0000
Solution quality estimate total_estimate	0.6028
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.704
Kurtosis Kurtosis kurtosis	-0.291
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	772000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.083; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.016; Smooth: 0.566

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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	Protocadherin-15
Molecular weight formula_weight	43069.2 kDa
Mutation mutation	G16D N369D Q370N
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	2639

MQYDDDWQYEDCKLARDGPPATIVAIDEESRNGTILVDNMLIKGTAGGPDPTIELSLKDNVDYWVLMDPVKQMLFLNSTGRVLDRDPPMNIHSIVVQVQCINKKVGTIIYHEVRIVVRDRNDNSPTFKHESYYATVNELTPVGTTIFTGFSGDNGATDIDDGPNGQIEYVIQYNPDDPTSNDTFEIPLMLTGNIVLRKRLNYEDKTRYFVIIQANDRAQNLNERRTTTTTLTVDVLDGDDLGPMFLPCVLVPNTRDCRPLTYQAAIPELRTPEELNPIIVTPPIQAIDQDRNIQPPSDRPGILYSILVGTPEDYPRFFHMHPRTAELSLLEPVNRDFHQKFDLVIKAEQDNGHPLPAFAGLHIEILDENDNLEHHHHHH

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 BL21

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6mfoA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3430 —

Domain ID domain_id	6mfoA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

Domain ID domain_id	6mfoA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

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8. Citations (1)

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Unit-cell length a length_a	87.894 Å
Unit-cell length b length_b	116.516 Å
Unit-cell length c length_c	99.889 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	49.990 Å
R factor r_factor	0.2181
R_work r_work	0.2145
R_free r_free	0.2884

fit	/app/data/saxs_computation/mf/6mfo/6mfo.fit
pddf	/app/data/pr_computation/mf/6mfo/6mfo.pr.out
profile	/app/data/saxs_computation/mf/6mfo/6mfo.dat

Crystal Structure of Human Protocadherin-15 EC1-3 G16D N369D Q370N

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

Protocadherin-15

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