SAXSdb — 9qgo

▼

1. Structure Basics

entry_id	9qgo
deposition_date	2025-03-14
title	Interaction between PlPVC1 baseplate and fiber in extended state
keywords	contractile injection system, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	18.75 Å
rg_electron	17.93 Å
i0	8588980.00
molecular_weight	21344.0 kDa
excluded_volume	26739 Å³
envelope_volume	33463 Å³
shell_volume	16246 Å³
envelope_diameter	63.5 Å
shell_rg	23.27 Å
envelope_rg	17.95 Å
shape_rg	17.91 Å
total_rg	18.92 Å
total_atoms	1505
n_residues	193
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

▼

3. P(r) Analysis (GNOM)

dmax	67.1 Å
rg_real	18.68 Å
rg_real_error	0.58 Å
i0_real	8.5890e+06
i0_real_error	1.1160e+05
rg_reciprocal	18.69 Å
i0_reciprocal	8589000.0000
total_estimate	0.7694
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.3 Å
skewness	0.229
kurtosis	-0.256
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	1345000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.674; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Tail fiber protein
formula_weight	45745.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	1505

MEKEHNPYNSETNLETNLENTNIKSTGPSADDLKSRFKEGSIPLQTDYADLIDIADIGRRAVGKAPDQTNNPNSALELDDNSGLKIKINSTGGLKADQDGLSVKLKDKSLLADPNGLAVNAGRGVKINNDQLEVDGYHGIEIVNEGVKVKASNGINVNSDGVSVKAGNGISVSGKGVEVKAKDKGSISVDSDGIAVKYWDGGGIVATDNSGLYLKLEGGNTNNGWSGVSGLSLSKNGVKVKAGNGITVDSSGVSIDPKTVLPKGMIVMFSGSSAPTGWAFCDGNHGTPDLRSRFVMCSETISETGKSSNKASGSGNGKNYSRNTTSTTVSVSVTVKNTTLTESQIPYHYHIGGMGYWTNKGMKYGTEYYSEYASYIRNDLDSVMQSANGARYAYTSPSGGGQGHNHPATASSPSHDHSVNVIPPYYLLAFIMKL

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

Entity 2 polymer

description	Baseplate protein J-like domain-containing protein
formula_weight	110905.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	a,b,c

MNNQDALFPIVKDDIAFETLLTQAKTVIEQQSGQLWSNTEENDPGITLLEACCYGASDLAYRHSLPLRDLLTPEKQEQTLGDGIFPQEFGPQQMLTCGPITAEDYRRALLDLHSSDTDNETSEDYFFFNDVRLICEPESERYKYWYNKESREYSFIQEQEQEQEQLQLTLRGNYWLYLLPNRETEDDKTLTQKRLNDFLKDNRNLGESVSKIIWLQPVDFLLQLDIELDDDVSDLADIFAQVYMTTEQMVLTSPLRYSTQAMIEQGYSNEEIFEGPYLHHGWIPELSAAKDYTKPTELKLSHLANRLLAIPGVQNITRLALGKHDENISPLADDSWSWTIAQGYYPRLWGNDPLDLISSSASPLTITAKGGVKITVSKQDIENKIIAEPLIETQPELLNWGKHRKVLDYYPVSNKLPACYGLQTYAETQQQVHLHQFMLPFEQMLANGCAELALLPKLLAFKQRGNTVYGTQWPFKANTVGQQVHQEIMPDLIKQLNNDSQINSDDGIHSQNYTKELSILNYLLEYFGTHRAARPLTLDSLDFLSTQRGYLAQQPELTYQRNNIRIDKVSALQKRIAARLGLGGKCFEETSKLDELPFYLIEHRQLLPVKPDTKFDKEQKPDKLKIKSVPNSKNQQLIITQNGTTGQLLYGQVINLIIKEKENQDIRVKFILRGQMITDITGESFILDTRNSTALARSLIDVQNAYNDGNLYWCNSPVWMEDMDYQLVYASEIYQTGTENERWITSSPQSPFPAMIEENDEITLKYVITPSGPKKSDHELKANVIKFDRIQGKILIKLTQDSQDNFPLAADAWRYRWYFSSEKYALADRFSFVVSMVINSQLVKNDDVDPYKLESWAKTEILAEFPAHLSMIIHWLSPEDFKDFVSTYQRWQNNGAPLGDEAYHVLETLTLGRLPSAATGIGNMRIATAQQRIGVVGESGKEWNTEVIISNQLVYVPYTGENLNKR

Source

organism	Photorhabdus luminescens
ncbi_taxonomy_id	29488
host_organism	Escherichia coli

▶

6. Citations (1)

▶

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	6.00 Å
resolution_method	—
num_particles	71148

fit	/app/data/saxs_computation/qg/9qgo/9qgo.fit
pddf	/app/data/pr_computation/qg/9qgo/9qgo.pr.out
profile	/app/data/saxs_computation/qg/9qgo/9qgo.dat

Interaction between PlPVC1 baseplate and fiber in extended state

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)