SAXSdb — 9ynb

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1. Structure Basics

entry_id	9ynb
deposition_date	2025-10-10
title	Structure of the T6SS effector protein PdpC
keywords	Francisella, T6SS, secretion, effector, TOXIN; TOXIN
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	37.58 Å
rg_electron	37.73 Å
i0	150545000.00
molecular_weight	105690.0 kDa
excluded_volume	135240 Å³
envelope_volume	180070 Å³
shell_volume	42600 Å³
envelope_diameter	136.9 Å
shell_rg	40.49 Å
envelope_rg	37.55 Å
shape_rg	37.72 Å
total_rg	37.98 Å
total_atoms	7462
n_residues	905
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	132.1 Å
rg_real	37.95 Å
rg_real_error	1.23 Å
i0_real	1.5050e+08
i0_real_error	2.9610e+06
rg_reciprocal	37.72 Å
i0_reciprocal	150500000.0000
total_estimate	0.8360
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.6 Å
skewness	0.542
kurtosis	-0.308
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	40730000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.845; Smooth: 0.837

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	T6SS effector protein PdpC
formula_weight	161288.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7462

MGSSHHHHHHSSGLVPRGSDYKDHDGDYKDHDIDYKDDDDKENLYFQGNDKYELNIYFEKIELPKTADFNMISKHDIKELRVDANLKKKIHLLQFDEDYLAYMRSLRAIHPSKIAMQKIKSIRNKEDSFIIAIFSLDKIIHKTKFISFGHKTVIFDFKKLWGLVDFVIVHTSNKTWVNHKLTSFMPSITYCNQNIIHLAYHSDFLYIYHTPEFMDDINVDRENRRELVAKIPDPYWVRADTKENKININSEEENIEKDLKKITKLKNFEISANDIFFSKAIKAAPRLQHKNKSKLFNSLAIENNEKIKRDIIDYAISNAWYKNEGLLENLMTFLDALVVRHLYLIAVYSVYEIEIGIKSVKPEYSKLLKAGLLNKDIQNQLIYDQKKISNIIWLGETFHGLDIEEAEDLCELIDQGDINPKINPINPEKLYRAYKENYGNEALSFREYKEKYNFLDNDKLREEHANKLSSILEDPKFRVLSYINAFLCSTKNYLVPYGYLGSNPLTYYNCMLETGKRRTSKEAYFADIRNKLFMVCYLPGFLSSVIADDDFIDWYSNKKENQELLKNSYLNNLYKSKQKYIKDFIDLDIIKLLKQTSSQIKPSYIPVAFRYGAFASTTALIRSNANVSNRMEFELYDSPERLHNQYSEKEEMIMPKSVNNPKDHSIDNGISLFSLNLTNEKEDGLRKVMLKVAQLYNLDFKVGISGNLDQAMTQALILGMATTKKNGDILLDEDQMLYMTYLYCIFMAHSVDHTVDEILMSANTYLLNSEEVKYPIFNIADFFARPVFGLSKDKEFKSLVEKYENSLKPNSKILKENYISRVVTLSEVYEVYEDLNCLYSSLSEGSLYNLLSTHSERHCTLLEQYSRKKKAEIGLVQDGEKIKVVNNYSGYAAINQYQRFVSLGRMYDSGAKYSSSHKKQIEKDFNLYLPDKEQINYLKYNFKDNKFDAVYKNKKSKEKNQSHIVYAKKQNTRYCYGYFNDFFVKNRITTFYKIKDKSGNYLVNLHNEKYSFATPNSDSKIYRVSPELLNNRDDFKRVSKDIIKSYKYISFDKQKEDIVKNFGKNLYHTNYEIWVGLSHQAISCFSVLDNIDTQEAANTFIDALYYVRLMQLYYGKTIPFLWISSEIVRYSSSETHYYIPTEENFENILKIALNNASKPVIERFLIILNIYNSTIDNNALILIRCRLPIILFEYEEQKLKLKALQKCADSYKKNNYKNEINFSAWFESIFHVQNLSLSPNYIGNNILILSLVEELKPKCSEYKKNMINQQITAKANELNFYQLLIRLIEISTYHRILTKSIITNTTSLLYDILNKPEFQTINKLINKLFIYKNKDLNTDKYKAFHTKLITIESTYKKINSLYKSDFFKKISS

Source

organism	Francisella tularensis subsp. novicida (strain U112)
ncbi_taxonomy_id	401614
host_organism	Francisella tularensis subsp. novicida (strain U112)

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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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	322627

fit	/app/data/saxs_computation/yn/9ynb/9ynb.fit
pddf	/app/data/pr_computation/yn/9ynb/9ynb.pr.out
profile	/app/data/saxs_computation/yn/9ynb/9ynb.dat

Structure of the T6SS effector protein PdpC

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)