SAXSdb — 9xou

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1. Structure Basics

entry_id	9xou
deposition_date	2025-11-15
title	CryoEM structure of LacY with Trimbody
keywords	STRUCTURAL PROTEIN; STRUCTURAL 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	57.21 Å
rg_electron	58.14 Å
i0	1198320000.00
molecular_weight	316670.0 kDa
excluded_volume	406970 Å³
envelope_volume	599000 Å³
shell_volume	88371 Å³
envelope_diameter	167.9 Å
shell_rg	58.15 Å
envelope_rg	56.03 Å
shape_rg	58.21 Å
total_rg	57.84 Å
total_atoms	22382
n_residues	2870
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	156.4 Å
rg_real	56.94 Å
rg_real_error	0.99 Å
i0_real	1.1980e+09
i0_real_error	1.8210e+07
rg_reciprocal	57.40 Å
i0_reciprocal	1199000000.0000
total_estimate	0.8461
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	92.7 Å
skewness	-0.039
kurtosis	-0.771
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	44750000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.999; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	H3-PrAC-5350A,2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase
formula_weight	36127.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	22382

MKEIAKIVAELLRGIARIIDDIKGRDREEEVEILAKAVEKTGKPEDVRLALEAAERGVTLDQAKAIAQILSMPNLTDEQKRGFVQSLLDDPSVSKEILAEAKKLNEHQAAKAEEAARKMEELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTVIKALSVLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPDEVREKAKAFVEKIRGCTEAAALEHHHHHH

Source

organism	Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
ncbi_taxonomy_id	243274
host_organism	Escherichia coli

Entity 2 polymer

description	LacY-nanobody-TAIL
formula_weight	28210.1 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

MQVQLVESGGRLVQAGDSLRLSCAASGRTFTTYLMGWFRQAPGKEREFVAAIRWSGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKLEDTAVYYCAAAARPSYSGDYGYTEALRYDYWGQGTLVAVVKTVEDAFLALLALEQHLGVQPADLAALAEKLNLSQLLELGELLKAAGHPLAPQVEALLKEKLKAASAAEAAGVIFQALVKDEELGKKILEWAKEFGTEEAKKAIEIAEKAYELYKKYGSWSHPQFEK

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 3 polymer

description	Lactose permease
formula_weight	49236.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,H,I

MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFSFNAGAPAVEAFIEKVSRRSNFEFGRARMFGAVGWALVASIVGIMFTINNQFVFWLGSGMALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSSTYDVFDQQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGSFKYITSQFEVRFSATIYLVAFAFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVAWSHPQFEKGSHHHHHHHHHH

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

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6. Citations (1)

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resolution	2.50 Å
resolution_method	—
num_particles	371100

fit	/app/data/saxs_computation/xo/9xou/9xou.fit
pddf	/app/data/pr_computation/xo/9xou/9xou.pr.out
profile	/app/data/saxs_computation/xo/9xou/9xou.dat

CryoEM structure of LacY with Trimbody

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

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)