SAXSdb — 9yap

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1. Structure Basics

entry_id	9yap
deposition_date	2025-09-16
title	Gbg crosslinked to PLCb3 - second conformation
keywords	G protein, heterotrimeric G protein, lipase, phospholipase, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	36.44 Å
rg_electron	35.87 Å
i0	252373000.00
molecular_weight	127600.0 kDa
excluded_volume	159430 Å³
envelope_volume	211790 Å³
shell_volume	49233 Å³
envelope_diameter	124.4 Å
shell_rg	42.62 Å
envelope_rg	34.99 Å
shape_rg	35.85 Å
total_rg	36.40 Å
total_atoms	14901
n_residues	1134
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	118.4 Å
rg_real	36.40 Å
rg_real_error	0.80 Å
i0_real	2.5240e+08
i0_real_error	3.7730e+06
rg_reciprocal	36.43 Å
i0_reciprocal	252400000.0000
total_estimate	0.6766
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	38.6 Å
skewness	0.246
kurtosis	-0.556
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	50580000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.983; Smooth: 0.891

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
formula_weight	99653.9 kDa
ec_number	3.1.4.11
mutation	E60C, S193C, S221C, S358C, S824C, S834C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	14901

MAHHHHHHGTALQLEPPTVVETLRRGSKFIKWDEETSSRNLVTLRVDPNGFFLYWTGPNMCVDTLDISSIRDTRTGRYARLPKDPKIREVLGFGGPDARLEEKLMTVVSGPDPVNTVFLNFMAVQDDTAKVWSEELFKLAMNILAQNASRNTFLRKAYTKLKLQVNQDGRIPVKNILKMFSADKKRVETALESSGLKFNRSESIRPDEFSLEIFERFLNKLSLRPDIDKILLEIGAKGKPYLTLEQLMDFINQKQRDPRLNEVLYPPLRPSQARLLIEKYEPNQQFLERDQMSMEGFSRYLGGEENGILPLEALDLSTDMTQPLSAYFINSSHNTYLTAGQLAGTSSVEMYRQALLWGSRCVELDVWKGRPPEEEPFITHGFTMTTEVPLRDVLEAIAETAFKTSPYPVILSFENHVDSAKQQAKMAEYCRSIFGDALLIEPLDKYPLAPGVPLPSPQDLMGRILVKNKKRHRPSAGGPDSAGRKRPLEQSNSALSESSAATEPSSPQLGSPSSDSCPGLSNGEEVGLEKPSLEPQKSLGDEGLNRGPYVLGPADREDEEEDEEEEEQTDPKKPTTDEGTASSEVNATEEMSTLVNYIEPVKFKSFEAARKRNKCFEMSSFVETKAMEQLTKSPMEFVEYNKQQLSRIYPKGTRVDSSNYMPQLFWNVGCQLVALNFQTLDVAMQLNAGVFEYNGRSGYLLKPEFMRRPDKSFDPFTEVIVDGIVANALRVKVISGQFLSDRKVGIYVEVDMFGLPVDTRRKYRTRTSQGNSFNPVWDEEPFDFPKVVLPTLASLRIAAFEEGGKFVGHRILPVSAIRSGYHYVSLRNEANQPLSLPALLIYTEASDYIPDDHQDYAEALINPIKHVSLMDQRARQLAALIGE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	37285.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Trichoplusia ni

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	7861.1 kDa
mutation	C68S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Trichoplusia ni

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	4.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.50 Å
resolution_method	—
num_particles	142175

fit	/app/data/saxs_computation/ya/9yap/9yap.fit
pddf	/app/data/pr_computation/ya/9yap/9yap.pr.out
profile	/app/data/saxs_computation/ya/9yap/9yap.dat

Gbg crosslinked to PLCb3 - second conformation

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)